Mon 24 Dec 07:56:56 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 2it9-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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/2it9-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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 07:57:00 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/2it9-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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 418 and 0 Target number of residues in the AU: 418 Target solvent content: 0.6240 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: 2it9-3.2-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: 2it9-3.2-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 3.200 Wilson plot Bfac: 63.35 10303 reflections ( 98.61 % complete ) and 0 restraints for refining 4529 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3714 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3041 (Rfree = 0.000) for 4529 atoms. Found 40 (40 requested) and removed 55 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 4596 seeds are put forward NCS extension: 0 residues added, 4596 seeds are put forward Round 1: 230 peptides, 43 chains. Longest chain 10 peptides. Score 0.345 Round 2: 277 peptides, 42 chains. Longest chain 14 peptides. Score 0.479 Round 3: 295 peptides, 42 chains. Longest chain 16 peptides. Score 0.522 Round 4: 306 peptides, 44 chains. Longest chain 21 peptides. Score 0.527 Round 5: 296 peptides, 38 chains. Longest chain 22 peptides. Score 0.563 Taking the results from Round 5 Chains 39, Residues 258, Estimated correctness of the model 30.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7923 restraints for refining 3710 atoms. 6883 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2671 (Rfree = 0.000) for 3710 atoms. Found 32 (33 requested) and removed 23 (16 requested) atoms. Cycle 2: After refmac, R = 0.2524 (Rfree = 0.000) for 3681 atoms. Found 22 (33 requested) and removed 20 (16 requested) atoms. Cycle 3: After refmac, R = 0.2489 (Rfree = 0.000) for 3665 atoms. Found 13 (33 requested) and removed 19 (16 requested) atoms. Cycle 4: After refmac, R = 0.2428 (Rfree = 0.000) for 3650 atoms. Found 8 (32 requested) and removed 19 (16 requested) atoms. Cycle 5: After refmac, R = 0.2414 (Rfree = 0.000) for 3634 atoms. Found 6 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3756 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3776 seeds are put forward Round 1: 276 peptides, 45 chains. Longest chain 15 peptides. Score 0.445 Round 2: 306 peptides, 42 chains. Longest chain 17 peptides. Score 0.546 Round 3: 304 peptides, 37 chains. Longest chain 18 peptides. Score 0.589 Round 4: 295 peptides, 39 chains. Longest chain 18 peptides. Score 0.551 Round 5: 297 peptides, 37 chains. Longest chain 31 peptides. Score 0.575 Taking the results from Round 3 Chains 37, Residues 267, Estimated correctness of the model 38.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8025 restraints for refining 3710 atoms. 6994 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2572 (Rfree = 0.000) for 3710 atoms. Found 33 (33 requested) and removed 19 (16 requested) atoms. Cycle 7: After refmac, R = 0.2442 (Rfree = 0.000) for 3706 atoms. Found 13 (33 requested) and removed 20 (16 requested) atoms. Cycle 8: After refmac, R = 0.2459 (Rfree = 0.000) for 3691 atoms. Found 6 (33 requested) and removed 18 (16 requested) atoms. Cycle 9: After refmac, R = 0.2366 (Rfree = 0.000) for 3673 atoms. Found 11 (33 requested) and removed 20 (16 requested) atoms. Cycle 10: After refmac, R = 0.2322 (Rfree = 0.000) for 3662 atoms. Found 9 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3790 seeds are put forward Round 1: 272 peptides, 46 chains. Longest chain 15 peptides. Score 0.423 Round 2: 297 peptides, 39 chains. Longest chain 26 peptides. Score 0.556 Round 3: 303 peptides, 37 chains. Longest chain 31 peptides. Score 0.587 Round 4: 288 peptides, 32 chains. Longest chain 29 peptides. Score 0.604 Round 5: 307 peptides, 41 chains. Longest chain 19 peptides. Score 0.558 Taking the results from Round 4 Chains 32, Residues 256, Estimated correctness of the model 42.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8129 restraints for refining 3710 atoms. 7137 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2514 (Rfree = 0.000) for 3710 atoms. Found 17 (33 requested) and removed 20 (16 requested) atoms. Cycle 12: After refmac, R = 0.2360 (Rfree = 0.000) for 3696 atoms. Found 6 (33 requested) and removed 18 (16 requested) atoms. Cycle 13: After refmac, R = 0.2378 (Rfree = 0.000) for 3681 atoms. Found 8 (33 requested) and removed 17 (16 requested) atoms. Cycle 14: After refmac, R = 0.2311 (Rfree = 0.000) for 3668 atoms. Found 9 (32 requested) and removed 16 (16 requested) atoms. Cycle 15: After refmac, R = 0.2235 (Rfree = 0.000) for 3659 atoms. Found 9 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 3782 seeds are put forward NCS extension: 51 residues added (2 deleted due to clashes), 3833 seeds are put forward Round 1: 282 peptides, 45 chains. Longest chain 26 peptides. Score 0.460 Round 2: 286 peptides, 41 chains. Longest chain 26 peptides. Score 0.511 Round 3: 300 peptides, 40 chains. Longest chain 28 peptides. Score 0.552 Round 4: 295 peptides, 38 chains. Longest chain 20 peptides. Score 0.561 Round 5: 298 peptides, 40 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 4 Chains 38, Residues 257, Estimated correctness of the model 30.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8058 restraints for refining 3710 atoms. 7068 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2432 (Rfree = 0.000) for 3710 atoms. Found 24 (33 requested) and removed 19 (16 requested) atoms. Cycle 17: After refmac, R = 0.2326 (Rfree = 0.000) for 3706 atoms. Found 8 (33 requested) and removed 19 (16 requested) atoms. Cycle 18: After refmac, R = 0.2291 (Rfree = 0.000) for 3692 atoms. Found 13 (33 requested) and removed 16 (16 requested) atoms. Cycle 19: After refmac, R = 0.2250 (Rfree = 0.000) for 3683 atoms. Found 11 (33 requested) and removed 17 (16 requested) atoms. Cycle 20: After refmac, R = 0.2176 (Rfree = 0.000) for 3671 atoms. Found 9 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3765 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3779 seeds are put forward Round 1: 245 peptides, 39 chains. Longest chain 15 peptides. Score 0.432 Round 2: 278 peptides, 36 chains. Longest chain 21 peptides. Score 0.544 Round 3: 292 peptides, 39 chains. Longest chain 15 peptides. Score 0.545 Round 4: 277 peptides, 38 chains. Longest chain 13 peptides. Score 0.521 Round 5: 278 peptides, 36 chains. Longest chain 20 peptides. Score 0.544 Taking the results from Round 3 Chains 41, Residues 253, Estimated correctness of the model 25.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7951 restraints for refining 3710 atoms. 6927 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2512 (Rfree = 0.000) for 3710 atoms. Found 28 (33 requested) and removed 19 (16 requested) atoms. Cycle 22: After refmac, R = 0.2370 (Rfree = 0.000) for 3709 atoms. Found 14 (33 requested) and removed 17 (16 requested) atoms. Cycle 23: After refmac, R = 0.2324 (Rfree = 0.000) for 3702 atoms. Found 18 (33 requested) and removed 17 (16 requested) atoms. Cycle 24: After refmac, R = 0.2281 (Rfree = 0.000) for 3701 atoms. Found 9 (33 requested) and removed 16 (16 requested) atoms. Cycle 25: After refmac, R = 0.2252 (Rfree = 0.000) for 3692 atoms. Found 6 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3783 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3786 seeds are put forward Round 1: 255 peptides, 37 chains. Longest chain 14 peptides. Score 0.480 Round 2: 304 peptides, 44 chains. Longest chain 15 peptides. Score 0.522 Round 3: 297 peptides, 40 chains. Longest chain 15 peptides. Score 0.546 Round 4: 295 peptides, 36 chains. Longest chain 19 peptides. Score 0.580 Round 5: 283 peptides, 35 chains. Longest chain 18 peptides. Score 0.565 Taking the results from Round 4 Chains 36, Residues 259, Estimated correctness of the model 35.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7949 restraints for refining 3710 atoms. 6949 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2380 (Rfree = 0.000) for 3710 atoms. Found 21 (33 requested) and removed 18 (16 requested) atoms. Cycle 27: After refmac, R = 0.2311 (Rfree = 0.000) for 3701 atoms. Found 11 (33 requested) and removed 21 (16 requested) atoms. Cycle 28: After refmac, R = 0.2275 (Rfree = 0.000) for 3684 atoms. Found 17 (33 requested) and removed 16 (16 requested) atoms. Cycle 29: After refmac, R = 0.2219 (Rfree = 0.000) for 3684 atoms. Found 4 (33 requested) and removed 17 (16 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2215 (Rfree = 0.000) for 3667 atoms. Found 15 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3802 seeds are put forward Round 1: 247 peptides, 41 chains. Longest chain 11 peptides. Score 0.415 Round 2: 275 peptides, 40 chains. Longest chain 15 peptides. Score 0.496 Round 3: 278 peptides, 39 chains. Longest chain 16 peptides. Score 0.513 Round 4: 285 peptides, 36 chains. Longest chain 20 peptides. Score 0.559 Round 5: 284 peptides, 36 chains. Longest chain 15 peptides. Score 0.557 Taking the results from Round 4 Chains 36, Residues 249, Estimated correctness of the model 29.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8126 restraints for refining 3710 atoms. 7166 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2507 (Rfree = 0.000) for 3710 atoms. Found 21 (33 requested) and removed 16 (16 requested) atoms. Cycle 32: After refmac, R = 0.2346 (Rfree = 0.000) for 3707 atoms. Found 10 (33 requested) and removed 17 (16 requested) atoms. Cycle 33: After refmac, R = 0.2321 (Rfree = 0.000) for 3693 atoms. Found 13 (33 requested) and removed 17 (16 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2242 (Rfree = 0.000) for 3689 atoms. Found 10 (33 requested) and removed 18 (16 requested) atoms. Cycle 35: After refmac, R = 0.2238 (Rfree = 0.000) for 3677 atoms. Found 11 (33 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3789 seeds are put forward Round 1: 250 peptides, 44 chains. Longest chain 11 peptides. Score 0.388 Round 2: 270 peptides, 40 chains. Longest chain 12 peptides. Score 0.484 Round 3: 279 peptides, 37 chains. Longest chain 20 peptides. Score 0.536 Round 4: 276 peptides, 42 chains. Longest chain 20 peptides. Score 0.477 Round 5: 270 peptides, 38 chains. Longest chain 20 peptides. Score 0.505 Taking the results from Round 3 Chains 37, Residues 242, Estimated correctness of the model 22.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8126 restraints for refining 3710 atoms. 7195 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2463 (Rfree = 0.000) for 3710 atoms. Found 18 (33 requested) and removed 17 (16 requested) atoms. Cycle 37: After refmac, R = 0.2337 (Rfree = 0.000) for 3703 atoms. Found 15 (33 requested) and removed 17 (16 requested) atoms. Cycle 38: After refmac, R = 0.2363 (Rfree = 0.000) for 3697 atoms. Found 14 (33 requested) and removed 17 (16 requested) atoms. Cycle 39: After refmac, R = 0.2270 (Rfree = 0.000) for 3691 atoms. Found 8 (33 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.2297 (Rfree = 0.000) for 3678 atoms. Found 11 (33 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 3806 seeds are put forward Round 1: 231 peptides, 41 chains. Longest chain 12 peptides. Score 0.372 Round 2: 247 peptides, 36 chains. Longest chain 18 peptides. Score 0.471 Round 3: 256 peptides, 39 chains. Longest chain 20 peptides. Score 0.460 Round 4: 246 peptides, 36 chains. Longest chain 20 peptides. Score 0.468 Round 5: 251 peptides, 37 chains. Longest chain 14 peptides. Score 0.470 Taking the results from Round 2 Chains 36, Residues 211, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8231 restraints for refining 3710 atoms. 7423 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2324 (Rfree = 0.000) for 3710 atoms. Found 25 (33 requested) and removed 19 (16 requested) atoms. Cycle 42: After refmac, R = 0.2268 (Rfree = 0.000) for 3707 atoms. Found 19 (33 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.2172 (Rfree = 0.000) for 3708 atoms. Found 10 (33 requested) and removed 17 (16 requested) atoms. Cycle 44: After refmac, R = 0.2214 (Rfree = 0.000) for 3697 atoms. Found 23 (33 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.2090 (Rfree = 0.000) for 3703 atoms. Found 14 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3792 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3808 seeds are put forward Round 1: 225 peptides, 41 chains. Longest chain 13 peptides. Score 0.355 Round 2: 253 peptides, 35 chains. Longest chain 20 peptides. Score 0.496 Round 3: 248 peptides, 32 chains. Longest chain 20 peptides. Score 0.517 Round 4: 258 peptides, 36 chains. Longest chain 15 peptides. Score 0.498 Round 5: 256 peptides, 38 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 216, Estimated correctness of the model 16.8 % 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. 10303 reflections ( 98.61 % complete ) and 8193 restraints for refining 3710 atoms. 7361 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2222 (Rfree = 0.000) for 3710 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2221 (Rfree = 0.000) for 3687 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2221 (Rfree = 0.000) for 3668 atoms. Found 0 (32 requested) and removed 14 (16 requested) atoms. Cycle 49: After refmac, R = 0.2186 (Rfree = 0.000) for 3653 atoms. TimeTaking 42.07