Sun 23 Dec 22:22:46 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 1z85-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.4-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/1z85-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.4-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 22:22:56 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/1z85-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.4-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 391 and 0 Target number of residues in the AU: 391 Target solvent content: 0.6328 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-3.4-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: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.70 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: 65.199 3.400 Wilson plot Bfac: 67.74 8357 reflections ( 99.77 % complete ) and 0 restraints for refining 4137 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3242 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3222 (Rfree = 0.000) for 4137 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 4176 seeds are put forward NCS extension: 0 residues added, 4176 seeds are put forward Round 1: 208 peptides, 32 chains. Longest chain 19 peptides. Score 0.424 Round 2: 263 peptides, 34 chains. Longest chain 19 peptides. Score 0.541 Round 3: 292 peptides, 31 chains. Longest chain 40 peptides. Score 0.633 Round 4: 304 peptides, 32 chains. Longest chain 35 peptides. Score 0.647 Round 5: 311 peptides, 33 chains. Longest chain 50 peptides. Score 0.652 Taking the results from Round 5 Chains 33, Residues 278, Estimated correctness of the model 44.7 % 2 chains (58 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 6774 restraints for refining 3403 atoms. 5444 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2840 (Rfree = 0.000) for 3403 atoms. Found 18 (25 requested) and removed 44 (12 requested) atoms. Cycle 2: After refmac, R = 0.2740 (Rfree = 0.000) for 3277 atoms. Found 19 (25 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2652 (Rfree = 0.000) for 3240 atoms. Found 12 (24 requested) and removed 20 (12 requested) atoms. Cycle 4: After refmac, R = 0.2604 (Rfree = 0.000) for 3213 atoms. Found 9 (24 requested) and removed 19 (12 requested) atoms. Cycle 5: After refmac, R = 0.2584 (Rfree = 0.000) for 3188 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 3289 seeds are put forward NCS extension: 70 residues added (4 deleted due to clashes), 3359 seeds are put forward Round 1: 282 peptides, 36 chains. Longest chain 32 peptides. Score 0.564 Round 2: 306 peptides, 32 chains. Longest chain 40 peptides. Score 0.651 Round 3: 305 peptides, 33 chains. Longest chain 23 peptides. Score 0.640 Round 4: 309 peptides, 30 chains. Longest chain 27 peptides. Score 0.674 Round 5: 308 peptides, 32 chains. Longest chain 28 peptides. Score 0.655 Taking the results from Round 4 Chains 30, Residues 279, Estimated correctness of the model 50.9 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7164 restraints for refining 3348 atoms. 6054 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2872 (Rfree = 0.000) for 3348 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 7: After refmac, R = 0.2731 (Rfree = 0.000) for 3317 atoms. Found 12 (25 requested) and removed 15 (12 requested) atoms. Cycle 8: After refmac, R = 0.2567 (Rfree = 0.000) for 3299 atoms. Found 8 (25 requested) and removed 15 (12 requested) atoms. Cycle 9: After refmac, R = 0.2601 (Rfree = 0.000) for 3280 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.2543 (Rfree = 0.000) for 3271 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 3389 seeds are put forward NCS extension: 36 residues added (12 deleted due to clashes), 3425 seeds are put forward Round 1: 264 peptides, 33 chains. Longest chain 19 peptides. Score 0.554 Round 2: 293 peptides, 32 chains. Longest chain 31 peptides. Score 0.626 Round 3: 290 peptides, 34 chains. Longest chain 51 peptides. Score 0.601 Round 4: 301 peptides, 36 chains. Longest chain 46 peptides. Score 0.605 Round 5: 298 peptides, 32 chains. Longest chain 48 peptides. Score 0.636 Taking the results from Round 5 Chains 32, Residues 266, Estimated correctness of the model 40.0 % 2 chains (50 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 6811 restraints for refining 3403 atoms. 5554 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2709 (Rfree = 0.000) for 3403 atoms. Found 16 (25 requested) and removed 24 (12 requested) atoms. Cycle 12: After refmac, R = 0.2529 (Rfree = 0.000) for 3374 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 13: After refmac, R = 0.2465 (Rfree = 0.000) for 3355 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 14: After refmac, R = 0.2411 (Rfree = 0.000) for 3339 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.2392 (Rfree = 0.000) for 3325 atoms. Found 7 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 3428 seeds are put forward NCS extension: 74 residues added (9 deleted due to clashes), 3502 seeds are put forward Round 1: 255 peptides, 32 chains. Longest chain 22 peptides. Score 0.544 Round 2: 286 peptides, 35 chains. Longest chain 36 peptides. Score 0.583 Round 3: 280 peptides, 35 chains. Longest chain 26 peptides. Score 0.570 Round 4: 278 peptides, 37 chains. Longest chain 26 peptides. Score 0.545 Round 5: 285 peptides, 32 chains. Longest chain 39 peptides. Score 0.610 Taking the results from Round 5 Chains 32, Residues 253, Estimated correctness of the model 31.9 % 1 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7264 restraints for refining 3404 atoms. 6120 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2586 (Rfree = 0.000) for 3404 atoms. Found 14 (25 requested) and removed 25 (12 requested) atoms. Cycle 17: After refmac, R = 0.2435 (Rfree = 0.000) for 3376 atoms. Found 3 (25 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2388 (Rfree = 0.000) for 3358 atoms. Found 6 (25 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.2336 (Rfree = 0.000) for 3346 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2311 (Rfree = 0.000) for 3337 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 3422 seeds are put forward NCS extension: 76 residues added (3 deleted due to clashes), 3498 seeds are put forward Round 1: 259 peptides, 39 chains. Longest chain 19 peptides. Score 0.477 Round 2: 280 peptides, 32 chains. Longest chain 31 peptides. Score 0.599 Round 3: 272 peptides, 35 chains. Longest chain 20 peptides. Score 0.552 Round 4: 282 peptides, 30 chains. Longest chain 19 peptides. Score 0.623 Round 5: 278 peptides, 29 chains. Longest chain 22 peptides. Score 0.624 Taking the results from Round 5 Chains 29, Residues 249, Estimated correctness of the model 36.3 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7285 restraints for refining 3404 atoms. 6260 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2409 (Rfree = 0.000) for 3404 atoms. Found 16 (25 requested) and removed 15 (12 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 3386 atoms. Found 3 (25 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.2243 (Rfree = 0.000) for 3367 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2204 (Rfree = 0.000) for 3357 atoms. Found 5 (25 requested) and removed 15 (12 requested) atoms. Cycle 25: After refmac, R = 0.2188 (Rfree = 0.000) for 3343 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 3443 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3462 seeds are put forward Round 1: 231 peptides, 34 chains. Longest chain 19 peptides. Score 0.462 Round 2: 272 peptides, 34 chains. Longest chain 25 peptides. Score 0.562 Round 3: 283 peptides, 35 chains. Longest chain 21 peptides. Score 0.576 Round 4: 278 peptides, 35 chains. Longest chain 22 peptides. Score 0.565 Round 5: 274 peptides, 33 chains. Longest chain 19 peptides. Score 0.577 Taking the results from Round 5 Chains 33, Residues 241, Estimated correctness of the model 21.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7170 restraints for refining 3403 atoms. 6131 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2380 (Rfree = 0.000) for 3403 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 27: After refmac, R = 0.2261 (Rfree = 0.000) for 3398 atoms. Found 10 (25 requested) and removed 21 (12 requested) atoms. Cycle 28: After refmac, R = 0.2304 (Rfree = 0.000) for 3379 atoms. Found 17 (25 requested) and removed 18 (12 requested) atoms. Cycle 29: After refmac, R = 0.2121 (Rfree = 0.000) for 3364 atoms. Found 8 (25 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2100 (Rfree = 0.000) for 3351 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.02 Search for helices and strands: 0 residues in 0 chains, 3458 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 3472 seeds are put forward Round 1: 220 peptides, 33 chains. Longest chain 27 peptides. Score 0.445 Round 2: 248 peptides, 31 chains. Longest chain 16 peptides. Score 0.538 Round 3: 259 peptides, 34 chains. Longest chain 23 peptides. Score 0.532 Round 4: 266 peptides, 34 chains. Longest chain 30 peptides. Score 0.548 Round 5: 276 peptides, 33 chains. Longest chain 26 peptides. Score 0.581 Taking the results from Round 5 Chains 35, Residues 243, Estimated correctness of the model 22.4 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7042 restraints for refining 3404 atoms. 5912 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2384 (Rfree = 0.000) for 3404 atoms. Found 22 (25 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.2233 (Rfree = 0.000) for 3391 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. Cycle 33: After refmac, R = 0.2205 (Rfree = 0.000) for 3377 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2187 (Rfree = 0.000) for 3367 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 35: After refmac, R = 0.2329 (Rfree = 0.000) for 3357 atoms. Found 16 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 3431 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3448 seeds are put forward Round 1: 224 peptides, 38 chains. Longest chain 18 peptides. Score 0.395 Round 2: 242 peptides, 35 chains. Longest chain 19 peptides. Score 0.479 Round 3: 257 peptides, 33 chains. Longest chain 21 peptides. Score 0.538 Round 4: 264 peptides, 32 chains. Longest chain 22 peptides. Score 0.565 Round 5: 249 peptides, 33 chains. Longest chain 23 peptides. Score 0.519 Taking the results from Round 4 Chains 33, Residues 232, Estimated correctness of the model 16.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7362 restraints for refining 3403 atoms. 6421 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2452 (Rfree = 0.000) for 3403 atoms. Found 19 (25 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.2309 (Rfree = 0.000) for 3402 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 38: After refmac, R = 0.2267 (Rfree = 0.000) for 3392 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2237 (Rfree = 0.000) for 3383 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2261 (Rfree = 0.000) for 3375 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.05 Search for helices and strands: 0 residues in 0 chains, 3441 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 3475 seeds are put forward Round 1: 217 peptides, 37 chains. Longest chain 14 peptides. Score 0.388 Round 2: 255 peptides, 36 chains. Longest chain 23 peptides. Score 0.501 Round 3: 256 peptides, 35 chains. Longest chain 24 peptides. Score 0.514 Round 4: 252 peptides, 35 chains. Longest chain 20 peptides. Score 0.504 Round 5: 263 peptides, 32 chains. Longest chain 27 peptides. Score 0.562 Taking the results from Round 5 Chains 32, Residues 231, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8357 reflections ( 99.77 % complete ) and 7547 restraints for refining 3403 atoms. 6655 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2412 (Rfree = 0.000) for 3403 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 42: After refmac, R = 0.2274 (Rfree = 0.000) for 3393 atoms. Found 9 (25 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2140 (Rfree = 0.000) for 3388 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2180 (Rfree = 0.000) for 3374 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.2093 (Rfree = 0.000) for 3365 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.02 Search for helices and strands: 0 residues in 0 chains, 3439 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3463 seeds are put forward Round 1: 235 peptides, 33 chains. Longest chain 24 peptides. Score 0.484 Round 2: 259 peptides, 34 chains. Longest chain 25 peptides. Score 0.532 Round 3: 266 peptides, 33 chains. Longest chain 21 peptides. Score 0.559 Round 4: 269 peptides, 35 chains. Longest chain 24 peptides. Score 0.545 Round 5: 260 peptides, 37 chains. Longest chain 21 peptides. Score 0.502 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 233, Estimated correctness of the model 14.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1z85-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8357 reflections ( 99.77 % complete ) and 7563 restraints for refining 3404 atoms. 6664 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2295 (Rfree = 0.000) for 3404 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2178 (Rfree = 0.000) for 3387 atoms. Found 0 (25 requested) and removed 9 (12 requested) atoms. Cycle 48: After refmac, R = 0.2176 (Rfree = 0.000) for 3375 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2121 (Rfree = 0.000) for 3362 atoms. TimeTaking 56.7