null Tue 25 Dec 19:27:55 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 1z85-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.6-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/1z85-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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/1z85-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.6-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.6432 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: 1z85-3.6-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: 1z85-3.6-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 3.600 Wilson plot Bfac: 73.41 7071 reflections ( 99.73 % complete ) and 0 restraints for refining 4139 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3318 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3464 (Rfree = 0.000) for 4139 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 4197 seeds are put forward NCS extension: 0 residues added, 4197 seeds are put forward Round 1: 192 peptides, 33 chains. Longest chain 17 peptides. Score 0.366 Round 2: 243 peptides, 31 chains. Longest chain 21 peptides. Score 0.526 Round 3: 263 peptides, 32 chains. Longest chain 22 peptides. Score 0.562 Round 4: 271 peptides, 33 chains. Longest chain 24 peptides. Score 0.570 Round 5: 271 peptides, 29 chains. Longest chain 27 peptides. Score 0.610 Taking the results from Round 5 Chains 29, Residues 242, Estimated correctness of the model 18.5 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7511 restraints for refining 3394 atoms. 6499 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3102 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 2: After refmac, R = 0.2991 (Rfree = 0.000) for 3309 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 3: After refmac, R = 0.2950 (Rfree = 0.000) for 3236 atoms. Found 16 (21 requested) and removed 28 (10 requested) atoms. Cycle 4: After refmac, R = 0.2821 (Rfree = 0.000) for 3184 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 5: After refmac, R = 0.2474 (Rfree = 0.000) for 3152 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 3278 seeds are put forward Round 1: 260 peptides, 37 chains. Longest chain 19 peptides. Score 0.502 Round 2: 288 peptides, 40 chains. Longest chain 21 peptides. Score 0.537 Round 3: 278 peptides, 34 chains. Longest chain 27 peptides. Score 0.575 Round 4: 282 peptides, 33 chains. Longest chain 28 peptides. Score 0.594 Round 5: 288 peptides, 33 chains. Longest chain 28 peptides. Score 0.606 Taking the results from Round 5 Chains 33, Residues 255, Estimated correctness of the model 17.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7135 restraints for refining 3353 atoms. 6099 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2703 (Rfree = 0.000) for 3353 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 7: After refmac, R = 0.2624 (Rfree = 0.000) for 3297 atoms. Found 18 (21 requested) and removed 25 (10 requested) atoms. Cycle 8: After refmac, R = 0.2633 (Rfree = 0.000) for 3259 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 9: After refmac, R = 0.2578 (Rfree = 0.000) for 3232 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 10: After refmac, R = 0.2648 (Rfree = 0.000) for 3211 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 3346 seeds are put forward NCS extension: 41 residues added (8 deleted due to clashes), 3387 seeds are put forward Round 1: 263 peptides, 34 chains. Longest chain 18 peptides. Score 0.541 Round 2: 283 peptides, 32 chains. Longest chain 27 peptides. Score 0.606 Round 3: 303 peptides, 37 chains. Longest chain 30 peptides. Score 0.600 Round 4: 293 peptides, 32 chains. Longest chain 23 peptides. Score 0.626 Round 5: 289 peptides, 34 chains. Longest chain 28 peptides. Score 0.599 Taking the results from Round 4 Chains 33, Residues 261, Estimated correctness of the model 24.5 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7087 restraints for refining 3379 atoms. 5977 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2597 (Rfree = 0.000) for 3379 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 12: After refmac, R = 0.2429 (Rfree = 0.000) for 3344 atoms. Found 16 (21 requested) and removed 22 (10 requested) atoms. Cycle 13: After refmac, R = 0.2320 (Rfree = 0.000) for 3324 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 14: After refmac, R = 0.2425 (Rfree = 0.000) for 3310 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 15: After refmac, R = 0.2224 (Rfree = 0.000) for 3305 atoms. Found 16 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 3413 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3433 seeds are put forward Round 1: 260 peptides, 42 chains. Longest chain 15 peptides. Score 0.446 Round 2: 279 peptides, 36 chains. Longest chain 24 peptides. Score 0.557 Round 3: 267 peptides, 34 chains. Longest chain 19 peptides. Score 0.551 Round 4: 286 peptides, 36 chains. Longest chain 23 peptides. Score 0.573 Round 5: 277 peptides, 31 chains. Longest chain 40 peptides. Score 0.603 Taking the results from Round 5 Chains 33, Residues 246, Estimated correctness of the model 15.8 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7151 restraints for refining 3393 atoms. 6087 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2693 (Rfree = 0.000) for 3393 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 17: After refmac, R = 0.2602 (Rfree = 0.000) for 3345 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 18: After refmac, R = 0.2628 (Rfree = 0.000) for 3305 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 19: After refmac, R = 0.2614 (Rfree = 0.000) for 3284 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 20: After refmac, R = 0.2534 (Rfree = 0.000) for 3262 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 3361 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 3380 seeds are put forward Round 1: 235 peptides, 35 chains. Longest chain 15 peptides. Score 0.461 Round 2: 262 peptides, 34 chains. Longest chain 22 peptides. Score 0.539 Round 3: 278 peptides, 35 chains. Longest chain 23 peptides. Score 0.565 Round 4: 295 peptides, 34 chains. Longest chain 31 peptides. Score 0.611 Round 5: 286 peptides, 32 chains. Longest chain 31 peptides. Score 0.612 Taking the results from Round 5 Chains 32, Residues 254, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7440 restraints for refining 3392 atoms. 6456 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2779 (Rfree = 0.000) for 3392 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.2818 (Rfree = 0.000) for 3363 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 23: After refmac, R = 0.2590 (Rfree = 0.000) for 3336 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 24: After refmac, R = 0.2566 (Rfree = 0.000) for 3322 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 25: After refmac, R = 0.2448 (Rfree = 0.000) for 3319 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 3426 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3460 seeds are put forward Round 1: 227 peptides, 41 chains. Longest chain 13 peptides. Score 0.367 Round 2: 255 peptides, 38 chains. Longest chain 19 peptides. Score 0.478 Round 3: 268 peptides, 34 chains. Longest chain 22 peptides. Score 0.553 Round 4: 252 peptides, 31 chains. Longest chain 22 peptides. Score 0.548 Round 5: 261 peptides, 28 chains. Longest chain 23 peptides. Score 0.598 Taking the results from Round 5 Chains 29, Residues 233, Estimated correctness of the model 13.9 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7402 restraints for refining 3394 atoms. 6430 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2641 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.2555 (Rfree = 0.000) for 3378 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 28: After refmac, R = 0.2449 (Rfree = 0.000) for 3363 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 29: After refmac, R = 0.2450 (Rfree = 0.000) for 3357 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 30: After refmac, R = 0.2324 (Rfree = 0.000) for 3352 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 3462 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3487 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 11 peptides. Score 0.336 Round 2: 226 peptides, 34 chains. Longest chain 18 peptides. Score 0.449 Round 3: 226 peptides, 34 chains. Longest chain 20 peptides. Score 0.449 Round 4: 238 peptides, 35 chains. Longest chain 13 peptides. Score 0.469 Round 5: 248 peptides, 34 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 5 Chains 34, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7593 restraints for refining 3394 atoms. 6771 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2885 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.2661 (Rfree = 0.000) for 3367 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 33: After refmac, R = 0.2649 (Rfree = 0.000) for 3348 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.2725 (Rfree = 0.000) for 3337 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 35: After refmac, R = 0.2557 (Rfree = 0.000) for 3326 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 3432 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3449 seeds are put forward Round 1: 192 peptides, 36 chains. Longest chain 11 peptides. Score 0.326 Round 2: 224 peptides, 36 chains. Longest chain 16 peptides. Score 0.419 Round 3: 238 peptides, 37 chains. Longest chain 17 peptides. Score 0.446 Round 4: 238 peptides, 34 chains. Longest chain 18 peptides. Score 0.480 Round 5: 239 peptides, 32 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 5 Chains 32, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7615 restraints for refining 3394 atoms. 6819 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2708 (Rfree = 0.000) for 3394 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 37: After refmac, R = 0.2861 (Rfree = 0.000) for 3360 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 38: After refmac, R = 0.2727 (Rfree = 0.000) for 3344 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.2785 (Rfree = 0.000) for 3329 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 40: After refmac, R = 0.2708 (Rfree = 0.000) for 3321 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 3447 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3466 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 13 peptides. Score 0.314 Round 2: 213 peptides, 32 chains. Longest chain 19 peptides. Score 0.438 Round 3: 206 peptides, 32 chains. Longest chain 17 peptides. Score 0.419 Round 4: 218 peptides, 32 chains. Longest chain 17 peptides. Score 0.451 Round 5: 228 peptides, 33 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 33, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7071 reflections ( 99.73 % complete ) and 7621 restraints for refining 3393 atoms. 6874 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2709 (Rfree = 0.000) for 3393 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 42: After refmac, R = 0.2560 (Rfree = 0.000) for 3370 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 43: After refmac, R = 0.2689 (Rfree = 0.000) for 3350 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.2745 (Rfree = 0.000) for 3343 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 45: After refmac, R = 0.2899 (Rfree = 0.000) for 3329 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 3454 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3477 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 11 peptides. Score 0.293 Round 2: 161 peptides, 28 chains. Longest chain 12 peptides. Score 0.338 Round 3: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.348 Round 4: 175 peptides, 30 chains. Longest chain 13 peptides. Score 0.354 Round 5: 176 peptides, 31 chains. Longest chain 11 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 145, 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 1z85-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7071 reflections ( 99.73 % complete ) and 7616 restraints for refining 3309 atoms. 7066 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2790 (Rfree = 0.000) for 3309 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2726 (Rfree = 0.000) for 3283 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2789 (Rfree = 0.000) for 3263 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2748 (Rfree = 0.000) for 3241 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:29:00 GMT 2018 Job finished. TimeTaking 61.09 Used memory is bytes: 8094376