Sun 23 Dec 22:23:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vp7-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-4.0-parrot-hancs/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-hancs.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-hancs.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 5284 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3162 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3406 (Rfree = 0.000) for 5284 atoms. Found 25 (25 requested) and removed 38 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 5374 seeds are put forward NCS extension: 0 residues added, 5374 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 11 peptides. Score 0.279 Round 2: 220 peptides, 31 chains. Longest chain 21 peptides. Score 0.435 Round 3: 236 peptides, 29 chains. Longest chain 20 peptides. Score 0.492 Round 4: 224 peptides, 26 chains. Longest chain 16 peptides. Score 0.496 Round 5: 247 peptides, 27 chains. Longest chain 17 peptides. Score 0.535 Taking the results from Round 5 Chains 28, Residues 220, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 9193 restraints for refining 3939 atoms. 8283 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2609 (Rfree = 0.000) for 3939 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. Cycle 2: After refmac, R = 0.2397 (Rfree = 0.000) for 3798 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. Cycle 3: After refmac, R = 0.2198 (Rfree = 0.000) for 3710 atoms. Found 15 (17 requested) and removed 29 (8 requested) atoms. Cycle 4: After refmac, R = 0.2421 (Rfree = 0.000) for 3637 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2295 (Rfree = 0.000) for 3592 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3791 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3810 seeds are put forward Round 1: 225 peptides, 42 chains. Longest chain 11 peptides. Score 0.327 Round 2: 238 peptides, 34 chains. Longest chain 12 peptides. Score 0.445 Round 3: 231 peptides, 33 chains. Longest chain 14 peptides. Score 0.439 Round 4: 234 peptides, 32 chains. Longest chain 13 peptides. Score 0.456 Round 5: 246 peptides, 29 chains. Longest chain 20 peptides. Score 0.513 Taking the results from Round 5 Chains 29, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8064 restraints for refining 3584 atoms. 7225 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2706 (Rfree = 0.000) for 3584 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Cycle 7: After refmac, R = 0.2388 (Rfree = 0.000) for 3509 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 8: After refmac, R = 0.2311 (Rfree = 0.000) for 3458 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 9: After refmac, R = 0.2140 (Rfree = 0.000) for 3419 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 10: After refmac, R = 0.1822 (Rfree = 0.000) for 3400 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3547 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3570 seeds are put forward Round 1: 217 peptides, 36 chains. Longest chain 14 peptides. Score 0.373 Round 2: 242 peptides, 36 chains. Longest chain 18 peptides. Score 0.433 Round 3: 237 peptides, 32 chains. Longest chain 19 peptides. Score 0.463 Round 4: 241 peptides, 35 chains. Longest chain 14 peptides. Score 0.441 Round 5: 235 peptides, 32 chains. Longest chain 20 peptides. Score 0.459 Taking the results from Round 3 Chains 33, Residues 205, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 7664 restraints for refining 3535 atoms. 6811 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2242 (Rfree = 0.000) for 3535 atoms. Found 15 (16 requested) and removed 26 (8 requested) atoms. Cycle 12: After refmac, R = 0.2098 (Rfree = 0.000) for 3501 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 13: After refmac, R = 0.2147 (Rfree = 0.000) for 3473 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 14: After refmac, R = 0.2066 (Rfree = 0.000) for 3450 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 15: After refmac, R = 0.1971 (Rfree = 0.000) for 3420 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 3623 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3642 seeds are put forward Round 1: 221 peptides, 37 chains. Longest chain 11 peptides. Score 0.372 Round 2: 224 peptides, 30 chains. Longest chain 16 peptides. Score 0.455 Round 3: 230 peptides, 30 chains. Longest chain 18 peptides. Score 0.468 Round 4: 227 peptides, 30 chains. Longest chain 15 peptides. Score 0.461 Round 5: 230 peptides, 26 chains. Longest chain 23 peptides. Score 0.509 Taking the results from Round 5 Chains 26, Residues 204, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8391 restraints for refining 3746 atoms. 7579 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2904 (Rfree = 0.000) for 3746 atoms. Found 17 (17 requested) and removed 54 (8 requested) atoms. Cycle 17: After refmac, R = 0.2679 (Rfree = 0.000) for 3648 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 18: After refmac, R = 0.2627 (Rfree = 0.000) for 3556 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 19: After refmac, R = 0.2498 (Rfree = 0.000) for 3492 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 20: After refmac, R = 0.2390 (Rfree = 0.000) for 3458 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.36 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3684 seeds are put forward Round 1: 208 peptides, 39 chains. Longest chain 11 peptides. Score 0.316 Round 2: 243 peptides, 38 chains. Longest chain 12 peptides. Score 0.415 Round 3: 240 peptides, 36 chains. Longest chain 17 peptides. Score 0.429 Round 4: 245 peptides, 35 chains. Longest chain 19 peptides. Score 0.451 Round 5: 252 peptides, 38 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 4 Chains 35, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8129 restraints for refining 3633 atoms. 7324 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2854 (Rfree = 0.000) for 3633 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 22: After refmac, R = 0.2610 (Rfree = 0.000) for 3568 atoms. Found 13 (17 requested) and removed 28 (8 requested) atoms. Cycle 23: After refmac, R = 0.2428 (Rfree = 0.000) for 3522 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 24: After refmac, R = 0.2428 (Rfree = 0.000) for 3490 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 25: After refmac, R = 0.2345 (Rfree = 0.000) for 3471 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 3661 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3680 seeds are put forward Round 1: 196 peptides, 37 chains. Longest chain 11 peptides. Score 0.307 Round 2: 250 peptides, 41 chains. Longest chain 13 peptides. Score 0.400 Round 3: 248 peptides, 36 chains. Longest chain 19 peptides. Score 0.447 Round 4: 238 peptides, 37 chains. Longest chain 17 peptides. Score 0.413 Round 5: 246 peptides, 36 chains. Longest chain 16 peptides. Score 0.443 Taking the results from Round 3 Chains 36, Residues 212, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 7839 restraints for refining 3591 atoms. 6943 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2410 (Rfree = 0.000) for 3591 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 27: After refmac, R = 0.2319 (Rfree = 0.000) for 3526 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 28: After refmac, R = 0.2249 (Rfree = 0.000) for 3496 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 29: After refmac, R = 0.2329 (Rfree = 0.000) for 3474 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 30: After refmac, R = 0.2274 (Rfree = 0.000) for 3448 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 3682 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3712 seeds are put forward Round 1: 186 peptides, 39 chains. Longest chain 9 peptides. Score 0.256 Round 2: 209 peptides, 38 chains. Longest chain 10 peptides. Score 0.330 Round 3: 223 peptides, 38 chains. Longest chain 13 peptides. Score 0.366 Round 4: 226 peptides, 38 chains. Longest chain 22 peptides. Score 0.374 Round 5: 219 peptides, 36 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 5 Chains 36, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8469 restraints for refining 3679 atoms. 7773 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2713 (Rfree = 0.000) for 3679 atoms. Found 17 (17 requested) and removed 49 (8 requested) atoms. Cycle 32: After refmac, R = 0.2257 (Rfree = 0.000) for 3609 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 33: After refmac, R = 0.2318 (Rfree = 0.000) for 3578 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 34: After refmac, R = 0.2249 (Rfree = 0.000) for 3557 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 35: After refmac, R = 0.2128 (Rfree = 0.000) for 3541 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3724 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3738 seeds are put forward Round 1: 176 peptides, 38 chains. Longest chain 9 peptides. Score 0.240 Round 2: 222 peptides, 40 chains. Longest chain 12 peptides. Score 0.342 Round 3: 228 peptides, 40 chains. Longest chain 13 peptides. Score 0.357 Round 4: 239 peptides, 38 chains. Longest chain 12 peptides. Score 0.405 Round 5: 231 peptides, 35 chains. Longest chain 19 peptides. Score 0.418 Taking the results from Round 5 Chains 35, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8070 restraints for refining 3655 atoms. 7321 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2412 (Rfree = 0.000) for 3655 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 37: After refmac, R = 0.2295 (Rfree = 0.000) for 3602 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 38: After refmac, R = 0.2250 (Rfree = 0.000) for 3568 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 39: After refmac, R = 0.2128 (Rfree = 0.000) for 3534 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 40: After refmac, R = 0.2248 (Rfree = 0.000) for 3516 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 3.36 Search for helices and strands: 0 residues in 0 chains, 3731 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3753 seeds are put forward Round 1: 197 peptides, 40 chains. Longest chain 9 peptides. Score 0.275 Round 2: 224 peptides, 35 chains. Longest chain 14 peptides. Score 0.401 Round 3: 222 peptides, 37 chains. Longest chain 13 peptides. Score 0.375 Round 4: 236 peptides, 33 chains. Longest chain 16 peptides. Score 0.451 Round 5: 228 peptides, 32 chains. Longest chain 20 peptides. Score 0.443 Taking the results from Round 4 Chains 33, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6430 reflections ( 99.47 % complete ) and 8264 restraints for refining 3674 atoms. 7485 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2558 (Rfree = 0.000) for 3674 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 42: After refmac, R = 0.2367 (Rfree = 0.000) for 3635 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 43: After refmac, R = 0.2280 (Rfree = 0.000) for 3603 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 44: After refmac, R = 0.2130 (Rfree = 0.000) for 3569 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.2186 (Rfree = 0.000) for 3557 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3742 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3759 seeds are put forward Round 1: 205 peptides, 40 chains. Longest chain 10 peptides. Score 0.297 Round 2: 228 peptides, 36 chains. Longest chain 14 peptides. Score 0.400 Round 3: 215 peptides, 36 chains. Longest chain 14 peptides. Score 0.368 Round 4: 218 peptides, 31 chains. Longest chain 23 peptides. Score 0.430 Round 5: 225 peptides, 35 chains. Longest chain 16 peptides. Score 0.404 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 187, 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 8332 restraints for refining 3678 atoms. 7615 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2638 (Rfree = 0.000) for 3678 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2414 (Rfree = 0.000) for 3627 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2153 (Rfree = 0.000) for 3600 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2263 (Rfree = 0.000) for 3580 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 72.07