null Mon 24 Dec 00:13:58 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 2p7i-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-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/2p7i-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-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 00:14:03 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/2p7i-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-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 365 and 0 Target number of residues in the AU: 365 Target solvent content: 0.6386 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.2-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: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.200 Wilson plot Bfac: 71.18 9471 reflections ( 99.79 % complete ) and 0 restraints for refining 4449 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3134 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3201 (Rfree = 0.000) for 4449 atoms. Found 29 (39 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 4536 seeds are put forward NCS extension: 0 residues added, 4536 seeds are put forward Round 1: 233 peptides, 38 chains. Longest chain 20 peptides. Score 0.430 Round 2: 286 peptides, 41 chains. Longest chain 16 peptides. Score 0.535 Round 3: 304 peptides, 41 chains. Longest chain 20 peptides. Score 0.578 Round 4: 324 peptides, 40 chains. Longest chain 26 peptides. Score 0.630 Round 5: 324 peptides, 33 chains. Longest chain 24 peptides. Score 0.691 Taking the results from Round 5 Chains 35, Residues 291, Estimated correctness of the model 63.2 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7473 restraints for refining 3651 atoms. 6171 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2765 (Rfree = 0.000) for 3651 atoms. Found 23 (32 requested) and removed 31 (16 requested) atoms. Cycle 2: After refmac, R = 0.2601 (Rfree = 0.000) for 3580 atoms. Found 11 (32 requested) and removed 20 (16 requested) atoms. Cycle 3: After refmac, R = 0.2581 (Rfree = 0.000) for 3542 atoms. Found 4 (32 requested) and removed 19 (16 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 3505 atoms. Found 9 (31 requested) and removed 16 (15 requested) atoms. Cycle 5: After refmac, R = 0.2400 (Rfree = 0.000) for 3484 atoms. Found 10 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.23 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3615 seeds are put forward Round 1: 307 peptides, 40 chains. Longest chain 18 peptides. Score 0.594 Round 2: 323 peptides, 37 chains. Longest chain 28 peptides. Score 0.655 Round 3: 342 peptides, 37 chains. Longest chain 25 peptides. Score 0.690 Round 4: 318 peptides, 32 chains. Longest chain 29 peptides. Score 0.689 Round 5: 327 peptides, 31 chains. Longest chain 32 peptides. Score 0.713 Taking the results from Round 5 Chains 34, Residues 296, Estimated correctness of the model 67.9 % 3 chains (58 residues) have been docked in sequence Building loops using Loopy2018 34 chains (296 residues) following loop building 3 chains (58 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7577 restraints for refining 3650 atoms. 6206 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2604 (Rfree = 0.000) for 3650 atoms. Found 16 (32 requested) and removed 25 (16 requested) atoms. Cycle 7: After refmac, R = 0.2617 (Rfree = 0.000) for 3603 atoms. Found 14 (31 requested) and removed 17 (16 requested) atoms. Cycle 8: After refmac, R = 0.2546 (Rfree = 0.000) for 3588 atoms. Found 16 (31 requested) and removed 18 (16 requested) atoms. Cycle 9: After refmac, R = 0.2492 (Rfree = 0.000) for 3570 atoms. Found 16 (30 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.2470 (Rfree = 0.000) for 3550 atoms. Found 12 (29 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.24 Search for helices and strands: 0 residues in 0 chains, 3658 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3678 seeds are put forward Round 1: 284 peptides, 38 chains. Longest chain 26 peptides. Score 0.562 Round 2: 330 peptides, 32 chains. Longest chain 27 peptides. Score 0.710 Round 3: 332 peptides, 29 chains. Longest chain 25 peptides. Score 0.736 Round 4: 327 peptides, 30 chains. Longest chain 41 peptides. Score 0.720 Round 5: 334 peptides, 34 chains. Longest chain 23 peptides. Score 0.700 Taking the results from Round 3 Chains 31, Residues 303, Estimated correctness of the model 72.4 % 3 chains (22 residues) have been docked in sequence Building loops using Loopy2018 31 chains (303 residues) following loop building 3 chains (22 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7718 restraints for refining 3613 atoms. 6446 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2615 (Rfree = 0.000) for 3613 atoms. Found 14 (29 requested) and removed 28 (16 requested) atoms. Cycle 12: After refmac, R = 0.2486 (Rfree = 0.000) for 3576 atoms. Found 11 (28 requested) and removed 23 (16 requested) atoms. Cycle 13: After refmac, R = 0.2484 (Rfree = 0.000) for 3553 atoms. Found 15 (27 requested) and removed 25 (15 requested) atoms. Cycle 14: After refmac, R = 0.2320 (Rfree = 0.000) for 3539 atoms. Found 5 (26 requested) and removed 20 (15 requested) atoms. Cycle 15: After refmac, R = 0.2249 (Rfree = 0.000) for 3519 atoms. Found 4 (25 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.22 Search for helices and strands: 0 residues in 0 chains, 3601 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3623 seeds are put forward Round 1: 288 peptides, 36 chains. Longest chain 18 peptides. Score 0.592 Round 2: 313 peptides, 36 chains. Longest chain 26 peptides. Score 0.645 Round 3: 315 peptides, 37 chains. Longest chain 28 peptides. Score 0.639 Round 4: 338 peptides, 34 chains. Longest chain 29 peptides. Score 0.707 Round 5: 329 peptides, 35 chains. Longest chain 24 peptides. Score 0.683 Taking the results from Round 4 Chains 36, Residues 304, Estimated correctness of the model 66.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7864 restraints for refining 3652 atoms. 6598 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2724 (Rfree = 0.000) for 3652 atoms. Found 15 (26 requested) and removed 69 (16 requested) atoms. Cycle 17: After refmac, R = 0.2542 (Rfree = 0.000) for 3584 atoms. Found 25 (25 requested) and removed 20 (16 requested) atoms. Cycle 18: After refmac, R = 0.2262 (Rfree = 0.000) for 3577 atoms. Found 10 (24 requested) and removed 19 (16 requested) atoms. Cycle 19: After refmac, R = 0.2186 (Rfree = 0.000) for 3559 atoms. Found 3 (24 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.2049 (Rfree = 0.000) for 3540 atoms. Found 2 (22 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.26 Search for helices and strands: 0 residues in 0 chains, 3650 seeds are put forward NCS extension: 33 residues added (8 deleted due to clashes), 3683 seeds are put forward Round 1: 290 peptides, 46 chains. Longest chain 18 peptides. Score 0.491 Round 2: 314 peptides, 35 chains. Longest chain 24 peptides. Score 0.656 Round 3: 315 peptides, 32 chains. Longest chain 28 peptides. Score 0.684 Round 4: 316 peptides, 30 chains. Longest chain 29 peptides. Score 0.702 Round 5: 317 peptides, 34 chains. Longest chain 29 peptides. Score 0.670 Taking the results from Round 4 Chains 32, Residues 286, Estimated correctness of the model 65.6 % 2 chains (47 residues) have been docked in sequence Building loops using Loopy2018 32 chains (286 residues) following loop building 2 chains (47 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7470 restraints for refining 3652 atoms. 6151 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2489 (Rfree = 0.000) for 3652 atoms. Found 17 (22 requested) and removed 25 (16 requested) atoms. Cycle 22: After refmac, R = 0.2221 (Rfree = 0.000) for 3634 atoms. Found 7 (22 requested) and removed 22 (16 requested) atoms. Cycle 23: After refmac, R = 0.2193 (Rfree = 0.000) for 3609 atoms. Found 7 (21 requested) and removed 21 (16 requested) atoms. Cycle 24: After refmac, R = 0.2059 (Rfree = 0.000) for 3590 atoms. Found 8 (20 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.1988 (Rfree = 0.000) for 3577 atoms. Found 5 (20 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 50 residues added (3 deleted due to clashes), 3729 seeds are put forward Round 1: 281 peptides, 36 chains. Longest chain 20 peptides. Score 0.576 Round 2: 294 peptides, 34 chains. Longest chain 20 peptides. Score 0.625 Round 3: 311 peptides, 39 chains. Longest chain 21 peptides. Score 0.613 Round 4: 304 peptides, 37 chains. Longest chain 17 peptides. Score 0.617 Round 5: 307 peptides, 39 chains. Longest chain 19 peptides. Score 0.604 Taking the results from Round 2 Chains 35, Residues 260, Estimated correctness of the model 47.6 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7764 restraints for refining 3652 atoms. 6597 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2251 (Rfree = 0.000) for 3652 atoms. Found 11 (19 requested) and removed 19 (16 requested) atoms. Cycle 27: After refmac, R = 0.2669 (Rfree = 0.000) for 3638 atoms. Found 19 (19 requested) and removed 24 (16 requested) atoms. Cycle 28: After refmac, R = 0.2532 (Rfree = 0.000) for 3627 atoms. Found 19 (19 requested) and removed 26 (16 requested) atoms. Cycle 29: After refmac, R = 0.2290 (Rfree = 0.000) for 3611 atoms. Found 19 (19 requested) and removed 16 (16 requested) atoms. Cycle 30: After refmac, R = 0.2019 (Rfree = 0.000) for 3605 atoms. Found 5 (19 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.25 Search for helices and strands: 0 residues in 0 chains, 3705 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3730 seeds are put forward Round 1: 255 peptides, 41 chains. Longest chain 20 peptides. Score 0.455 Round 2: 272 peptides, 35 chains. Longest chain 21 peptides. Score 0.566 Round 3: 298 peptides, 34 chains. Longest chain 22 peptides. Score 0.633 Round 4: 298 peptides, 35 chains. Longest chain 22 peptides. Score 0.623 Round 5: 287 peptides, 33 chains. Longest chain 27 peptides. Score 0.620 Taking the results from Round 3 Chains 36, Residues 264, Estimated correctness of the model 49.7 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7693 restraints for refining 3641 atoms. 6494 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2358 (Rfree = 0.000) for 3641 atoms. Found 17 (19 requested) and removed 26 (16 requested) atoms. Cycle 32: After refmac, R = 0.2263 (Rfree = 0.000) for 3619 atoms. Found 12 (19 requested) and removed 23 (16 requested) atoms. Cycle 33: After refmac, R = 0.2258 (Rfree = 0.000) for 3596 atoms. Found 14 (19 requested) and removed 21 (16 requested) atoms. Cycle 34: After refmac, R = 0.2300 (Rfree = 0.000) for 3580 atoms. Found 18 (19 requested) and removed 18 (16 requested) atoms. Cycle 35: After refmac, R = 0.2463 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.26 Search for helices and strands: 0 residues in 0 chains, 3694 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3708 seeds are put forward Round 1: 252 peptides, 36 chains. Longest chain 17 peptides. Score 0.506 Round 2: 276 peptides, 35 chains. Longest chain 25 peptides. Score 0.575 Round 3: 258 peptides, 32 chains. Longest chain 18 peptides. Score 0.565 Round 4: 257 peptides, 35 chains. Longest chain 25 peptides. Score 0.530 Round 5: 282 peptides, 33 chains. Longest chain 19 peptides. Score 0.609 Taking the results from Round 5 Chains 35, Residues 249, Estimated correctness of the model 43.5 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7744 restraints for refining 3652 atoms. 6683 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2464 (Rfree = 0.000) for 3652 atoms. Found 18 (19 requested) and removed 22 (16 requested) atoms. Cycle 37: After refmac, R = 0.2396 (Rfree = 0.000) for 3634 atoms. Found 17 (19 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.2360 (Rfree = 0.000) for 3622 atoms. Found 13 (19 requested) and removed 18 (16 requested) atoms. Cycle 39: After refmac, R = 0.2368 (Rfree = 0.000) for 3599 atoms. Found 19 (19 requested) and removed 17 (16 requested) atoms. Cycle 40: After refmac, R = 0.2319 (Rfree = 0.000) for 3599 atoms. Found 11 (19 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3712 seeds are put forward Round 1: 219 peptides, 37 chains. Longest chain 15 peptides. Score 0.402 Round 2: 261 peptides, 39 chains. Longest chain 19 peptides. Score 0.495 Round 3: 266 peptides, 34 chains. Longest chain 19 peptides. Score 0.562 Round 4: 270 peptides, 37 chains. Longest chain 25 peptides. Score 0.540 Round 5: 263 peptides, 41 chains. Longest chain 18 peptides. Score 0.477 Taking the results from Round 3 Chains 34, Residues 232, Estimated correctness of the model 30.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7848 restraints for refining 3535 atoms. 6954 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2677 (Rfree = 0.000) for 3535 atoms. Found 19 (19 requested) and removed 27 (15 requested) atoms. Cycle 42: After refmac, R = 0.2190 (Rfree = 0.000) for 3517 atoms. Found 14 (19 requested) and removed 20 (15 requested) atoms. Cycle 43: After refmac, R = 0.2099 (Rfree = 0.000) for 3500 atoms. Found 11 (19 requested) and removed 17 (15 requested) atoms. Cycle 44: After refmac, R = 0.2058 (Rfree = 0.000) for 3490 atoms. Found 4 (19 requested) and removed 17 (15 requested) atoms. Cycle 45: After refmac, R = 0.1975 (Rfree = 0.000) for 3471 atoms. Found 4 (19 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 3578 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3611 seeds are put forward Round 1: 221 peptides, 39 chains. Longest chain 13 peptides. Score 0.383 Round 2: 257 peptides, 38 chains. Longest chain 15 peptides. Score 0.496 Round 3: 264 peptides, 37 chains. Longest chain 15 peptides. Score 0.525 Round 4: 258 peptides, 35 chains. Longest chain 17 peptides. Score 0.532 Round 5: 258 peptides, 39 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 223, Estimated correctness of the model 21.4 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2p7i-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 170 A and 184 A 33 chains (229 residues) following loop building 1 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9471 reflections ( 99.79 % complete ) and 7871 restraints for refining 3646 atoms. 6875 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2396 (Rfree = 0.000) for 3646 atoms. Found 0 (19 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2465 (Rfree = 0.000) for 3625 atoms. Found 0 (19 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2219 (Rfree = 0.000) for 3601 atoms. Found 0 (19 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2151 (Rfree = 0.000) for 3582 atoms. Found 0 (19 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:14:44 GMT 2018 Job finished. TimeTaking 60.78 Used memory is bytes: 21387240