Mon 24 Dec 07:31:28 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fno-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-parrot-noncs ############### 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 07:31:33 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/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-parrot-noncs/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 403 and 0 Target number of residues in the AU: 403 Target solvent content: 0.6285 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.4-parrot-noncs.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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.75 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: 106.006 3.400 Wilson plot Bfac: 65.36 8176 reflections ( 99.32 % complete ) and 0 restraints for refining 4370 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3331 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2462 (Rfree = 0.000) for 4370 atoms. Found 15 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 4461 seeds are put forward NCS extension: 0 residues added, 4461 seeds are put forward Round 1: 256 peptides, 47 chains. Longest chain 9 peptides. Score 0.374 Round 2: 282 peptides, 38 chains. Longest chain 16 peptides. Score 0.539 Round 3: 290 peptides, 40 chains. Longest chain 16 peptides. Score 0.537 Round 4: 300 peptides, 37 chains. Longest chain 18 peptides. Score 0.588 Round 5: 296 peptides, 37 chains. Longest chain 16 peptides. Score 0.580 Taking the results from Round 4 Chains 37, Residues 263, Estimated correctness of the model 24.7 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8027 restraints for refining 3607 atoms. 6999 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2751 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 2: After refmac, R = 0.2584 (Rfree = 0.000) for 3574 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 3: After refmac, R = 0.2566 (Rfree = 0.000) for 3536 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 4: After refmac, R = 0.2467 (Rfree = 0.000) for 3515 atoms. Found 26 (26 requested) and removed 14 (13 requested) atoms. Cycle 5: After refmac, R = 0.2374 (Rfree = 0.000) for 3514 atoms. Found 25 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3701 seeds are put forward Round 1: 258 peptides, 45 chains. Longest chain 13 peptides. Score 0.403 Round 2: 296 peptides, 44 chains. Longest chain 17 peptides. Score 0.510 Round 3: 288 peptides, 43 chains. Longest chain 18 peptides. Score 0.501 Round 4: 303 peptides, 44 chains. Longest chain 29 peptides. Score 0.526 Round 5: 300 peptides, 40 chains. Longest chain 25 peptides. Score 0.559 Taking the results from Round 5 Chains 42, Residues 260, Estimated correctness of the model 14.7 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7854 restraints for refining 3608 atoms. 6791 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2485 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 7: After refmac, R = 0.2354 (Rfree = 0.000) for 3597 atoms. Found 23 (27 requested) and removed 21 (13 requested) atoms. Cycle 8: After refmac, R = 0.2297 (Rfree = 0.000) for 3579 atoms. Found 21 (27 requested) and removed 16 (13 requested) atoms. Cycle 9: After refmac, R = 0.2324 (Rfree = 0.000) for 3569 atoms. Found 23 (27 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2120 (Rfree = 0.000) for 3567 atoms. Found 7 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3699 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3711 seeds are put forward Round 1: 254 peptides, 48 chains. Longest chain 12 peptides. Score 0.356 Round 2: 291 peptides, 46 chains. Longest chain 13 peptides. Score 0.477 Round 3: 288 peptides, 43 chains. Longest chain 14 peptides. Score 0.501 Round 4: 283 peptides, 37 chains. Longest chain 20 peptides. Score 0.551 Round 5: 286 peptides, 40 chains. Longest chain 18 peptides. Score 0.528 Taking the results from Round 4 Chains 38, Residues 246, Estimated correctness of the model 11.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8337 restraints for refining 3606 atoms. 7370 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2490 (Rfree = 0.000) for 3606 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 12: After refmac, R = 0.2318 (Rfree = 0.000) for 3594 atoms. Found 21 (27 requested) and removed 23 (13 requested) atoms. Cycle 13: After refmac, R = 0.2213 (Rfree = 0.000) for 3584 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 14: After refmac, R = 0.2122 (Rfree = 0.000) for 3580 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. Cycle 15: After refmac, R = 0.2073 (Rfree = 0.000) for 3563 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3717 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3730 seeds are put forward Round 1: 238 peptides, 45 chains. Longest chain 9 peptides. Score 0.347 Round 2: 275 peptides, 41 chains. Longest chain 17 peptides. Score 0.491 Round 3: 290 peptides, 43 chains. Longest chain 19 peptides. Score 0.506 Round 4: 281 peptides, 41 chains. Longest chain 16 peptides. Score 0.505 Round 5: 284 peptides, 39 chains. Longest chain 16 peptides. Score 0.533 Taking the results from Round 5 Chains 39, Residues 245, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8284 restraints for refining 3608 atoms. 7343 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2525 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 17: After refmac, R = 0.2400 (Rfree = 0.000) for 3598 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 18: After refmac, R = 0.2165 (Rfree = 0.000) for 3595 atoms. Found 14 (27 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2146 (Rfree = 0.000) for 3587 atoms. Found 10 (27 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.2072 (Rfree = 0.000) for 3575 atoms. Found 4 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3727 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3744 seeds are put forward Round 1: 228 peptides, 42 chains. Longest chain 10 peptides. Score 0.355 Round 2: 250 peptides, 40 chains. Longest chain 16 peptides. Score 0.439 Round 3: 246 peptides, 36 chains. Longest chain 12 peptides. Score 0.474 Round 4: 249 peptides, 40 chains. Longest chain 18 peptides. Score 0.436 Round 5: 260 peptides, 38 chains. Longest chain 13 peptides. Score 0.487 Taking the results from Round 5 Chains 38, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8229 restraints for refining 3608 atoms. 7379 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2417 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 22: After refmac, R = 0.2432 (Rfree = 0.000) for 3601 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 23: After refmac, R = 0.2372 (Rfree = 0.000) for 3593 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 24: After refmac, R = 0.2263 (Rfree = 0.000) for 3580 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 25: After refmac, R = 0.2265 (Rfree = 0.000) for 3583 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3759 seeds are put forward Round 1: 202 peptides, 39 chains. Longest chain 11 peptides. Score 0.316 Round 2: 223 peptides, 35 chains. Longest chain 13 peptides. Score 0.425 Round 3: 230 peptides, 35 chains. Longest chain 11 peptides. Score 0.444 Round 4: 224 peptides, 32 chains. Longest chain 20 peptides. Score 0.463 Round 5: 245 peptides, 34 chains. Longest chain 23 peptides. Score 0.494 Taking the results from Round 5 Chains 34, Residues 211, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8233 restraints for refining 3608 atoms. 7411 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2566 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Cycle 27: After refmac, R = 0.2255 (Rfree = 0.000) for 3598 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 3599 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 29: After refmac, R = 0.2046 (Rfree = 0.000) for 3599 atoms. Found 11 (27 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.2110 (Rfree = 0.000) for 3589 atoms. Found 21 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3755 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3774 seeds are put forward Round 1: 224 peptides, 46 chains. Longest chain 9 peptides. Score 0.293 Round 2: 247 peptides, 39 chains. Longest chain 14 peptides. Score 0.442 Round 3: 253 peptides, 40 chains. Longest chain 14 peptides. Score 0.447 Round 4: 246 peptides, 39 chains. Longest chain 16 peptides. Score 0.440 Round 5: 257 peptides, 40 chains. Longest chain 14 peptides. Score 0.457 Taking the results from Round 5 Chains 40, Residues 217, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8243 restraints for refining 3608 atoms. 7397 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2483 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 32: After refmac, R = 0.2372 (Rfree = 0.000) for 3603 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 33: After refmac, R = 0.2513 (Rfree = 0.000) for 3602 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 34: After refmac, R = 0.2255 (Rfree = 0.000) for 3588 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.2427 (Rfree = 0.000) for 3591 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3789 seeds are put forward Round 1: 198 peptides, 41 chains. Longest chain 9 peptides. Score 0.278 Round 2: 209 peptides, 37 chains. Longest chain 12 peptides. Score 0.362 Round 3: 211 peptides, 35 chains. Longest chain 13 peptides. Score 0.392 Round 4: 203 peptides, 29 chains. Longest chain 15 peptides. Score 0.444 Round 5: 210 peptides, 34 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 4 Chains 30, Residues 174, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8448 restraints for refining 3607 atoms. 7722 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2435 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 37: After refmac, R = 0.2378 (Rfree = 0.000) for 3594 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 38: After refmac, R = 0.2497 (Rfree = 0.000) for 3592 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 39: After refmac, R = 0.2446 (Rfree = 0.000) for 3590 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 40: After refmac, R = 0.2597 (Rfree = 0.000) for 3584 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 3760 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3778 seeds are put forward Round 1: 186 peptides, 39 chains. Longest chain 10 peptides. Score 0.266 Round 2: 201 peptides, 34 chains. Longest chain 13 peptides. Score 0.376 Round 3: 201 peptides, 34 chains. Longest chain 12 peptides. Score 0.376 Round 4: 221 peptides, 34 chains. Longest chain 17 peptides. Score 0.432 Round 5: 217 peptides, 32 chains. Longest chain 17 peptides. Score 0.445 Taking the results from Round 5 Chains 32, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8411 restraints for refining 3608 atoms. 7703 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2432 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 42: After refmac, R = 0.2371 (Rfree = 0.000) for 3605 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 43: After refmac, R = 0.2468 (Rfree = 0.000) for 3598 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 44: After refmac, R = 0.2608 (Rfree = 0.000) for 3588 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 45: After refmac, R = 0.2275 (Rfree = 0.000) for 3583 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3719 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3739 seeds are put forward Round 1: 181 peptides, 37 chains. Longest chain 9 peptides. Score 0.277 Round 2: 202 peptides, 36 chains. Longest chain 11 peptides. Score 0.354 Round 3: 201 peptides, 37 chains. Longest chain 10 peptides. Score 0.338 Round 4: 206 peptides, 33 chains. Longest chain 14 peptides. Score 0.403 Round 5: 203 peptides, 34 chains. Longest chain 19 peptides. Score 0.382 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 173, 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 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8176 reflections ( 99.32 % complete ) and 8415 restraints for refining 3608 atoms. 7756 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2410 (Rfree = 0.000) for 3608 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2563 (Rfree = 0.000) for 3585 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2430 (Rfree = 0.000) for 3559 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2287 (Rfree = 0.000) for 3540 atoms. TimeTaking 46.5