Sun 23 Dec 22:22:41 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 2it9-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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/2it9-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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 22:22:51 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/2it9-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.4-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 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-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.4-parrot-hancs.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 4543 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3663 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2522 (Rfree = 0.000) for 4543 atoms. Found 23 (34 requested) and removed 37 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 4621 seeds are put forward NCS extension: 0 residues added, 4621 seeds are put forward Round 1: 237 peptides, 47 chains. Longest chain 8 peptides. Score 0.317 Round 2: 309 peptides, 47 chains. Longest chain 17 peptides. Score 0.503 Round 3: 291 peptides, 39 chains. Longest chain 17 peptides. Score 0.543 Round 4: 283 peptides, 38 chains. Longest chain 23 peptides. Score 0.535 Round 5: 285 peptides, 33 chains. Longest chain 28 peptides. Score 0.588 Taking the results from Round 5 Chains 33, Residues 252, Estimated correctness of the model 24.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8291 restraints for refining 3694 atoms. 7316 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2720 (Rfree = 0.000) for 3694 atoms. Found 24 (27 requested) and removed 24 (13 requested) atoms. Cycle 2: After refmac, R = 0.2675 (Rfree = 0.000) for 3664 atoms. Found 15 (27 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2560 (Rfree = 0.000) for 3636 atoms. Found 9 (27 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.2314 (Rfree = 0.000) for 3607 atoms. Found 10 (27 requested) and removed 17 (13 requested) atoms. Cycle 5: After refmac, R = 0.2270 (Rfree = 0.000) for 3594 atoms. Found 1 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 3702 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3727 seeds are put forward Round 1: 259 peptides, 44 chains. Longest chain 18 peptides. Score 0.412 Round 2: 273 peptides, 41 chains. Longest chain 15 peptides. Score 0.480 Round 3: 272 peptides, 40 chains. Longest chain 13 peptides. Score 0.489 Round 4: 278 peptides, 42 chains. Longest chain 23 peptides. Score 0.482 Round 5: 274 peptides, 37 chains. Longest chain 28 peptides. Score 0.525 Taking the results from Round 5 Chains 37, Residues 237, Estimated correctness of the model 2.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8291 restraints for refining 3695 atoms. 7380 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2731 (Rfree = 0.000) for 3695 atoms. Found 19 (27 requested) and removed 21 (13 requested) atoms. Cycle 7: After refmac, R = 0.2655 (Rfree = 0.000) for 3678 atoms. Found 15 (27 requested) and removed 21 (13 requested) atoms. Cycle 8: After refmac, R = 0.2614 (Rfree = 0.000) for 3661 atoms. Found 17 (27 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2293 (Rfree = 0.000) for 3648 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.2283 (Rfree = 0.000) for 3635 atoms. Found 4 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 3767 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3778 seeds are put forward Round 1: 259 peptides, 43 chains. Longest chain 24 peptides. Score 0.423 Round 2: 272 peptides, 39 chains. Longest chain 21 peptides. Score 0.499 Round 3: 279 peptides, 36 chains. Longest chain 23 peptides. Score 0.546 Round 4: 272 peptides, 38 chains. Longest chain 18 peptides. Score 0.510 Round 5: 281 peptides, 37 chains. Longest chain 24 peptides. Score 0.540 Taking the results from Round 3 Chains 36, Residues 243, Estimated correctness of the model 10.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8275 restraints for refining 3695 atoms. 7339 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2479 (Rfree = 0.000) for 3695 atoms. Found 19 (27 requested) and removed 13 (13 requested) atoms. Cycle 12: After refmac, R = 0.2511 (Rfree = 0.000) for 3696 atoms. Found 11 (27 requested) and removed 16 (13 requested) atoms. Cycle 13: After refmac, R = 0.2425 (Rfree = 0.000) for 3681 atoms. Found 14 (27 requested) and removed 17 (13 requested) atoms. Cycle 14: After refmac, R = 0.2355 (Rfree = 0.000) for 3668 atoms. Found 16 (27 requested) and removed 16 (13 requested) atoms. Cycle 15: After refmac, R = 0.2163 (Rfree = 0.000) for 3661 atoms. Found 10 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3800 seeds are put forward Round 1: 241 peptides, 41 chains. Longest chain 14 peptides. Score 0.399 Round 2: 249 peptides, 36 chains. Longest chain 28 peptides. Score 0.476 Round 3: 258 peptides, 38 chains. Longest chain 24 peptides. Score 0.476 Round 4: 271 peptides, 37 chains. Longest chain 20 peptides. Score 0.518 Round 5: 267 peptides, 35 chains. Longest chain 20 peptides. Score 0.529 Taking the results from Round 5 Chains 35, Residues 232, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8255 restraints for refining 3695 atoms. 7362 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2470 (Rfree = 0.000) for 3695 atoms. Found 11 (27 requested) and removed 22 (13 requested) atoms. Cycle 17: After refmac, R = 0.2410 (Rfree = 0.000) for 3664 atoms. Found 8 (27 requested) and removed 16 (13 requested) atoms. Cycle 18: After refmac, R = 0.2424 (Rfree = 0.000) for 3646 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.2303 (Rfree = 0.000) for 3636 atoms. Found 3 (27 requested) and removed 14 (13 requested) atoms. Cycle 20: After refmac, R = 0.2340 (Rfree = 0.000) for 3618 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3735 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3747 seeds are put forward Round 1: 224 peptides, 36 chains. Longest chain 18 peptides. Score 0.412 Round 2: 259 peptides, 34 chains. Longest chain 19 peptides. Score 0.521 Round 3: 261 peptides, 36 chains. Longest chain 19 peptides. Score 0.505 Round 4: 245 peptides, 31 chains. Longest chain 19 peptides. Score 0.520 Round 5: 256 peptides, 34 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 2 Chains 36, Residues 225, Estimated correctness of the model 0.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8144 restraints for refining 3695 atoms. 7251 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2496 (Rfree = 0.000) for 3695 atoms. Found 17 (27 requested) and removed 20 (13 requested) atoms. Cycle 22: After refmac, R = 0.2401 (Rfree = 0.000) for 3677 atoms. Found 14 (27 requested) and removed 16 (13 requested) atoms. Cycle 23: After refmac, R = 0.2320 (Rfree = 0.000) for 3668 atoms. Found 4 (27 requested) and removed 17 (13 requested) atoms. Cycle 24: After refmac, R = 0.2255 (Rfree = 0.000) for 3645 atoms. Found 5 (27 requested) and removed 18 (13 requested) atoms. Cycle 25: After refmac, R = 0.2184 (Rfree = 0.000) for 3626 atoms. Found 7 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3717 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3729 seeds are put forward Round 1: 219 peptides, 38 chains. Longest chain 12 peptides. Score 0.374 Round 2: 244 peptides, 34 chains. Longest chain 18 peptides. Score 0.486 Round 3: 249 peptides, 38 chains. Longest chain 16 peptides. Score 0.454 Round 4: 252 peptides, 37 chains. Longest chain 17 peptides. Score 0.472 Round 5: 261 peptides, 36 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 5 Chains 37, Residues 225, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8036 restraints for refining 3695 atoms. 7114 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 3695 atoms. Found 17 (27 requested) and removed 22 (13 requested) atoms. Cycle 27: After refmac, R = 0.2212 (Rfree = 0.000) for 3677 atoms. Found 2 (27 requested) and removed 16 (13 requested) atoms. Cycle 28: After refmac, R = 0.2151 (Rfree = 0.000) for 3659 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 29: After refmac, R = 0.2114 (Rfree = 0.000) for 3645 atoms. Found 2 (27 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.2078 (Rfree = 0.000) for 3631 atoms. Found 6 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3746 seeds are put forward Round 1: 237 peptides, 45 chains. Longest chain 12 peptides. Score 0.341 Round 2: 243 peptides, 38 chains. Longest chain 15 peptides. Score 0.438 Round 3: 257 peptides, 38 chains. Longest chain 16 peptides. Score 0.474 Round 4: 238 peptides, 35 chains. Longest chain 14 peptides. Score 0.460 Round 5: 250 peptides, 37 chains. Longest chain 14 peptides. Score 0.467 Taking the results from Round 3 Chains 38, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8158 restraints for refining 3694 atoms. 7320 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2274 (Rfree = 0.000) for 3694 atoms. Found 13 (27 requested) and removed 18 (13 requested) atoms. Cycle 32: After refmac, R = 0.2210 (Rfree = 0.000) for 3670 atoms. Found 10 (27 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.2125 (Rfree = 0.000) for 3660 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. Cycle 34: After refmac, R = 0.2135 (Rfree = 0.000) for 3646 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.2047 (Rfree = 0.000) for 3634 atoms. Found 9 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3733 seeds are put forward Round 1: 224 peptides, 45 chains. Longest chain 13 peptides. Score 0.303 Round 2: 235 peptides, 38 chains. Longest chain 13 peptides. Score 0.418 Round 3: 244 peptides, 40 chains. Longest chain 16 peptides. Score 0.418 Round 4: 232 peptides, 34 chains. Longest chain 16 peptides. Score 0.456 Round 5: 227 peptides, 34 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 4 Chains 34, Residues 198, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8111 restraints for refining 3695 atoms. 7325 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2328 (Rfree = 0.000) for 3695 atoms. Found 11 (27 requested) and removed 18 (13 requested) atoms. Cycle 37: After refmac, R = 0.2233 (Rfree = 0.000) for 3678 atoms. Found 10 (27 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.2157 (Rfree = 0.000) for 3664 atoms. Found 6 (27 requested) and removed 18 (13 requested) atoms. Cycle 39: After refmac, R = 0.2115 (Rfree = 0.000) for 3647 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.2118 (Rfree = 0.000) for 3634 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3747 seeds are put forward Round 1: 205 peptides, 39 chains. Longest chain 11 peptides. Score 0.322 Round 2: 253 peptides, 39 chains. Longest chain 20 peptides. Score 0.453 Round 3: 228 peptides, 36 chains. Longest chain 16 peptides. Score 0.422 Round 4: 241 peptides, 34 chains. Longest chain 21 peptides. Score 0.478 Round 5: 243 peptides, 40 chains. Longest chain 17 peptides. Score 0.416 Taking the results from Round 4 Chains 34, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8621 reflections ( 98.45 % complete ) and 8018 restraints for refining 3695 atoms. 7224 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2418 (Rfree = 0.000) for 3695 atoms. Found 15 (27 requested) and removed 23 (13 requested) atoms. Cycle 42: After refmac, R = 0.2409 (Rfree = 0.000) for 3676 atoms. Found 14 (27 requested) and removed 18 (13 requested) atoms. Cycle 43: After refmac, R = 0.2305 (Rfree = 0.000) for 3671 atoms. Found 11 (27 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.2266 (Rfree = 0.000) for 3658 atoms. Found 4 (27 requested) and removed 18 (13 requested) atoms. Cycle 45: After refmac, R = 0.2293 (Rfree = 0.000) for 3642 atoms. Found 13 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 3731 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3754 seeds are put forward Round 1: 194 peptides, 38 chains. Longest chain 11 peptides. Score 0.302 Round 2: 199 peptides, 35 chains. Longest chain 10 peptides. Score 0.355 Round 3: 200 peptides, 32 chains. Longest chain 21 peptides. Score 0.394 Round 4: 208 peptides, 33 chains. Longest chain 18 peptides. Score 0.404 Round 5: 208 peptides, 33 chains. Longest chain 20 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 175, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 4 % 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 8097 restraints for refining 3695 atoms. 7385 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2306 (Rfree = 0.000) for 3695 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2233 (Rfree = 0.000) for 3671 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2229 (Rfree = 0.000) for 3652 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2161 (Rfree = 0.000) for 3630 atoms. TimeTaking 58.13