Mon 24 Dec 07:27:50 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 2it9-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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/2it9-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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 07:27:54 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/2it9-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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: 0.6375 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.4-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 3.400 Wilson plot Bfac: 70.20 8621 reflections ( 98.45 % complete ) and 0 restraints for refining 4494 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3793 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3166 (Rfree = 0.000) for 4494 atoms. Found 33 (33 requested) and removed 76 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4521 seeds are put forward NCS extension: 0 residues added, 4521 seeds are put forward Round 1: 210 peptides, 41 chains. Longest chain 8 peptides. Score 0.312 Round 2: 250 peptides, 45 chains. Longest chain 12 peptides. Score 0.377 Round 3: 288 peptides, 46 chains. Longest chain 14 peptides. Score 0.464 Round 4: 289 peptides, 42 chains. Longest chain 14 peptides. Score 0.508 Round 5: 284 peptides, 42 chains. Longest chain 13 peptides. Score 0.496 Taking the results from Round 4 Chains 42, Residues 247, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8116 restraints for refining 3695 atoms. 7138 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2879 (Rfree = 0.000) for 3695 atoms. Found 18 (27 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2832 (Rfree = 0.000) for 3639 atoms. Found 13 (27 requested) and removed 23 (13 requested) atoms. Cycle 3: After refmac, R = 0.2484 (Rfree = 0.000) for 3616 atoms. Found 9 (27 requested) and removed 21 (13 requested) atoms. Cycle 4: After refmac, R = 0.2527 (Rfree = 0.000) for 3600 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. Cycle 5: After refmac, R = 0.2458 (Rfree = 0.000) for 3584 atoms. Found 6 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 3693 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3717 seeds are put forward Round 1: 245 peptides, 41 chains. Longest chain 18 peptides. Score 0.409 Round 2: 282 peptides, 38 chains. Longest chain 16 peptides. Score 0.533 Round 3: 276 peptides, 38 chains. Longest chain 19 peptides. Score 0.519 Round 4: 281 peptides, 39 chains. Longest chain 19 peptides. Score 0.520 Round 5: 284 peptides, 39 chains. Longest chain 15 peptides. Score 0.527 Taking the results from Round 2 Chains 39, Residues 244, Estimated correctness of the model 5.3 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8023 restraints for refining 3694 atoms. 7012 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2640 (Rfree = 0.000) for 3694 atoms. Found 21 (27 requested) and removed 26 (13 requested) atoms. Cycle 7: After refmac, R = 0.2605 (Rfree = 0.000) for 3674 atoms. Found 14 (27 requested) and removed 20 (13 requested) atoms. Cycle 8: After refmac, R = 0.2572 (Rfree = 0.000) for 3662 atoms. Found 12 (27 requested) and removed 21 (13 requested) atoms. Cycle 9: After refmac, R = 0.2544 (Rfree = 0.000) for 3645 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. Cycle 10: After refmac, R = 0.2375 (Rfree = 0.000) for 3625 atoms. Found 4 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3722 seeds are put forward Round 1: 253 peptides, 43 chains. Longest chain 13 peptides. Score 0.408 Round 2: 272 peptides, 39 chains. Longest chain 22 peptides. Score 0.499 Round 3: 281 peptides, 37 chains. Longest chain 24 peptides. Score 0.540 Round 4: 279 peptides, 37 chains. Longest chain 20 peptides. Score 0.536 Round 5: 287 peptides, 36 chains. Longest chain 29 peptides. Score 0.563 Taking the results from Round 5 Chains 36, Residues 251, Estimated correctness of the model 16.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8051 restraints for refining 3695 atoms. 7083 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2964 (Rfree = 0.000) for 3695 atoms. Found 23 (27 requested) and removed 24 (13 requested) atoms. Cycle 12: After refmac, R = 0.2806 (Rfree = 0.000) for 3676 atoms. Found 20 (27 requested) and removed 22 (13 requested) atoms. Cycle 13: After refmac, R = 0.2714 (Rfree = 0.000) for 3659 atoms. Found 16 (27 requested) and removed 21 (13 requested) atoms. Cycle 14: After refmac, R = 0.2622 (Rfree = 0.000) for 3640 atoms. Found 21 (27 requested) and removed 20 (13 requested) atoms. Cycle 15: After refmac, R = 0.2361 (Rfree = 0.000) for 3629 atoms. Found 4 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3733 seeds are put forward Round 1: 241 peptides, 45 chains. Longest chain 11 peptides. Score 0.352 Round 2: 271 peptides, 43 chains. Longest chain 16 peptides. Score 0.454 Round 3: 273 peptides, 41 chains. Longest chain 16 peptides. Score 0.480 Round 4: 270 peptides, 39 chains. Longest chain 15 peptides. Score 0.494 Round 5: 272 peptides, 39 chains. Longest chain 19 peptides. Score 0.499 Taking the results from Round 5 Chains 39, Residues 233, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8213 restraints for refining 3694 atoms. 7320 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2538 (Rfree = 0.000) for 3694 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. Cycle 17: After refmac, R = 0.2470 (Rfree = 0.000) for 3675 atoms. Found 15 (27 requested) and removed 17 (13 requested) atoms. Cycle 18: After refmac, R = 0.2422 (Rfree = 0.000) for 3665 atoms. Found 13 (27 requested) and removed 19 (13 requested) atoms. Cycle 19: After refmac, R = 0.2378 (Rfree = 0.000) for 3655 atoms. Found 16 (27 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2328 (Rfree = 0.000) for 3654 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3791 seeds are put forward Round 1: 223 peptides, 43 chains. Longest chain 10 peptides. Score 0.325 Round 2: 264 peptides, 39 chains. Longest chain 22 peptides. Score 0.480 Round 3: 268 peptides, 41 chains. Longest chain 18 peptides. Score 0.468 Round 4: 274 peptides, 39 chains. Longest chain 16 peptides. Score 0.504 Round 5: 269 peptides, 38 chains. Longest chain 14 peptides. Score 0.503 Taking the results from Round 4 Chains 40, Residues 235, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 7899 restraints for refining 3695 atoms. 6968 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2442 (Rfree = 0.000) for 3695 atoms. Found 15 (27 requested) and removed 17 (13 requested) atoms. Cycle 22: After refmac, R = 0.2312 (Rfree = 0.000) for 3679 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.2226 (Rfree = 0.000) for 3671 atoms. Found 9 (27 requested) and removed 17 (13 requested) atoms. Cycle 24: After refmac, R = 0.2156 (Rfree = 0.000) for 3658 atoms. Found 14 (27 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.2093 (Rfree = 0.000) for 3658 atoms. Found 8 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3742 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3756 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 9 peptides. Score 0.315 Round 2: 256 peptides, 43 chains. Longest chain 13 peptides. Score 0.416 Round 3: 257 peptides, 43 chains. Longest chain 13 peptides. Score 0.418 Round 4: 255 peptides, 43 chains. Longest chain 23 peptides. Score 0.413 Round 5: 255 peptides, 41 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 5 Chains 41, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8155 restraints for refining 3695 atoms. 7340 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2267 (Rfree = 0.000) for 3695 atoms. Found 21 (27 requested) and removed 15 (13 requested) atoms. Cycle 27: After refmac, R = 0.2151 (Rfree = 0.000) for 3690 atoms. Found 12 (27 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.2070 (Rfree = 0.000) for 3684 atoms. Found 12 (27 requested) and removed 14 (13 requested) atoms. Cycle 29: After refmac, R = 0.2036 (Rfree = 0.000) for 3681 atoms. Found 10 (27 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2027 (Rfree = 0.000) for 3675 atoms. Found 9 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3777 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3798 seeds are put forward Round 1: 198 peptides, 40 chains. Longest chain 15 peptides. Score 0.289 Round 2: 234 peptides, 41 chains. Longest chain 12 peptides. Score 0.380 Round 3: 231 peptides, 40 chains. Longest chain 15 peptides. Score 0.383 Round 4: 243 peptides, 39 chains. Longest chain 16 peptides. Score 0.427 Round 5: 255 peptides, 44 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 4 Chains 41, Residues 204, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8133 restraints for refining 3695 atoms. 7303 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2504 (Rfree = 0.000) for 3695 atoms. Found 17 (27 requested) and removed 18 (13 requested) atoms. Cycle 32: After refmac, R = 0.2522 (Rfree = 0.000) for 3680 atoms. Found 26 (27 requested) and removed 21 (13 requested) atoms. Cycle 33: After refmac, R = 0.2398 (Rfree = 0.000) for 3681 atoms. Found 15 (27 requested) and removed 15 (13 requested) atoms. Cycle 34: After refmac, R = 0.2310 (Rfree = 0.000) for 3674 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.2271 (Rfree = 0.000) for 3665 atoms. Found 11 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3749 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3768 seeds are put forward Round 1: 234 peptides, 43 chains. Longest chain 12 peptides. Score 0.356 Round 2: 276 peptides, 46 chains. Longest chain 15 peptides. Score 0.434 Round 3: 272 peptides, 45 chains. Longest chain 14 peptides. Score 0.435 Round 4: 260 peptides, 41 chains. Longest chain 15 peptides. Score 0.448 Round 5: 245 peptides, 40 chains. Longest chain 10 peptides. Score 0.421 Taking the results from Round 4 Chains 41, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8329 restraints for refining 3695 atoms. 7494 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2358 (Rfree = 0.000) for 3695 atoms. Found 16 (27 requested) and removed 13 (13 requested) atoms. Cycle 37: After refmac, R = 0.2300 (Rfree = 0.000) for 3686 atoms. Found 15 (27 requested) and removed 14 (13 requested) atoms. Cycle 38: After refmac, R = 0.2236 (Rfree = 0.000) for 3681 atoms. Found 12 (27 requested) and removed 15 (13 requested) atoms. Cycle 39: After refmac, R = 0.2181 (Rfree = 0.000) for 3672 atoms. Found 13 (27 requested) and removed 16 (13 requested) atoms. Cycle 40: After refmac, R = 0.2129 (Rfree = 0.000) for 3665 atoms. Found 11 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3750 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3771 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 13 peptides. Score 0.327 Round 2: 232 peptides, 38 chains. Longest chain 13 peptides. Score 0.410 Round 3: 245 peptides, 38 chains. Longest chain 16 peptides. Score 0.444 Round 4: 240 peptides, 42 chains. Longest chain 11 peptides. Score 0.384 Round 5: 248 peptides, 40 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 3 Chains 38, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8290 restraints for refining 3694 atoms. 7500 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2203 (Rfree = 0.000) for 3694 atoms. Found 14 (27 requested) and removed 13 (13 requested) atoms. Cycle 42: After refmac, R = 0.2103 (Rfree = 0.000) for 3694 atoms. Found 5 (27 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.2140 (Rfree = 0.000) for 3683 atoms. Found 8 (27 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.2115 (Rfree = 0.000) for 3676 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.2052 (Rfree = 0.000) for 3665 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3737 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3755 seeds are put forward Round 1: 197 peptides, 38 chains. Longest chain 11 peptides. Score 0.311 Round 2: 229 peptides, 38 chains. Longest chain 15 peptides. Score 0.402 Round 3: 228 peptides, 39 chains. Longest chain 15 peptides. Score 0.387 Round 4: 228 peptides, 35 chains. Longest chain 18 peptides. Score 0.434 Round 5: 220 peptides, 35 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 193, 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 2it9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8621 reflections ( 98.45 % complete ) and 8204 restraints for refining 3695 atoms. 7467 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2253 (Rfree = 0.000) for 3695 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2261 (Rfree = 0.000) for 3674 atoms. Found 0 (27 requested) and removed 11 (13 requested) atoms. Cycle 48: After refmac, R = 0.2254 (Rfree = 0.000) for 3662 atoms. Found 0 (27 requested) and removed 7 (13 requested) atoms. Cycle 49: After refmac, R = 0.2168 (Rfree = 0.000) for 3655 atoms. TimeTaking 41.4