Tue 25 Dec 19:27:57 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 1z85-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.2-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/1z85-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.2-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 19:28:07 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/1z85-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.2-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 399 and 0 Target number of residues in the AU: 399 Target solvent content: 0.6253 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: 1z85-3.2-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: 1z85-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.65 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 3.200 Wilson plot Bfac: 63.89 9974 reflections ( 99.81 % complete ) and 0 restraints for refining 4175 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3280 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3318 (Rfree = 0.000) for 4175 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 4230 seeds are put forward NCS extension: 0 residues added, 4230 seeds are put forward Round 1: 219 peptides, 37 chains. Longest chain 17 peptides. Score 0.393 Round 2: 271 peptides, 33 chains. Longest chain 21 peptides. Score 0.570 Round 3: 305 peptides, 36 chains. Longest chain 32 peptides. Score 0.613 Round 4: 300 peptides, 32 chains. Longest chain 35 peptides. Score 0.640 Round 5: 308 peptides, 35 chains. Longest chain 41 peptides. Score 0.628 Taking the results from Round 4 Chains 35, Residues 268, Estimated correctness of the model 51.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 7284 restraints for refining 3416 atoms. 6152 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2915 (Rfree = 0.000) for 3416 atoms. Found 26 (30 requested) and removed 30 (15 requested) atoms. Cycle 2: After refmac, R = 0.2876 (Rfree = 0.000) for 3348 atoms. Found 17 (30 requested) and removed 25 (15 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2773 (Rfree = 0.000) for 3308 atoms. Found 15 (29 requested) and removed 19 (14 requested) atoms. Cycle 4: After refmac, R = 0.2763 (Rfree = 0.000) for 3274 atoms. Found 20 (29 requested) and removed 21 (14 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2580 (Rfree = 0.000) for 3256 atoms. Found 12 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 3350 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 3376 seeds are put forward Round 1: 291 peptides, 37 chains. Longest chain 40 peptides. Score 0.574 Round 2: 322 peptides, 32 chains. Longest chain 41 peptides. Score 0.680 Round 3: 321 peptides, 32 chains. Longest chain 30 peptides. Score 0.678 Round 4: 326 peptides, 29 chains. Longest chain 33 peptides. Score 0.711 Round 5: 332 peptides, 32 chains. Longest chain 40 peptides. Score 0.697 Taking the results from Round 4 Chains 34, Residues 297, Estimated correctness of the model 67.5 % 4 chains (75 residues) have been docked in sequence Building loops using Loopy2018 34 chains (297 residues) following loop building 4 chains (75 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6382 restraints for refining 3417 atoms. 4911 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2931 (Rfree = 0.000) for 3417 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2771 (Rfree = 0.000) for 3376 atoms. Found 15 (29 requested) and removed 24 (15 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2732 (Rfree = 0.000) for 3340 atoms. Found 20 (29 requested) and removed 20 (15 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2639 (Rfree = 0.000) for 3317 atoms. Found 18 (27 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.2572 (Rfree = 0.000) for 3301 atoms. Found 9 (27 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.94 Search for helices and strands: 0 residues in 0 chains, 3370 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3389 seeds are put forward Round 1: 279 peptides, 32 chains. Longest chain 44 peptides. Score 0.597 Round 2: 315 peptides, 34 chains. Longest chain 30 peptides. Score 0.650 Round 3: 305 peptides, 32 chains. Longest chain 44 peptides. Score 0.649 Round 4: 300 peptides, 28 chains. Longest chain 45 peptides. Score 0.675 Round 5: 320 peptides, 31 chains. Longest chain 53 peptides. Score 0.685 Taking the results from Round 5 Chains 32, Residues 289, Estimated correctness of the model 61.9 % 4 chains (88 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6298 restraints for refining 3416 atoms. 4761 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2836 (Rfree = 0.000) for 3416 atoms. Found 27 (27 requested) and removed 37 (15 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2820 (Rfree = 0.000) for 3375 atoms. Found 10 (27 requested) and removed 19 (15 requested) atoms. Cycle 13: After refmac, R = 0.2754 (Rfree = 0.000) for 3342 atoms. Found 10 (27 requested) and removed 18 (15 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2745 (Rfree = 0.000) for 3320 atoms. Found 7 (26 requested) and removed 21 (14 requested) atoms. Cycle 15: After refmac, R = 0.2710 (Rfree = 0.000) for 3291 atoms. Found 16 (26 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 3375 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 3398 seeds are put forward Round 1: 299 peptides, 40 chains. Longest chain 30 peptides. Score 0.562 Round 2: 311 peptides, 35 chains. Longest chain 29 peptides. Score 0.634 Round 3: 318 peptides, 34 chains. Longest chain 34 peptides. Score 0.656 Round 4: 320 peptides, 35 chains. Longest chain 32 peptides. Score 0.651 Round 5: 317 peptides, 37 chains. Longest chain 30 peptides. Score 0.628 Taking the results from Round 3 Chains 34, Residues 284, Estimated correctness of the model 55.3 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9974 reflections ( 99.81 % complete ) and 7011 restraints for refining 3418 atoms. 5753 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2798 (Rfree = 0.000) for 3418 atoms. Found 27 (27 requested) and removed 25 (15 requested) atoms. Cycle 17: After refmac, R = 0.2829 (Rfree = 0.000) for 3400 atoms. Found 16 (27 requested) and removed 25 (15 requested) atoms. Cycle 18: After refmac, R = 0.2698 (Rfree = 0.000) for 3377 atoms. Found 6 (27 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2675 (Rfree = 0.000) for 3361 atoms. Found 8 (27 requested) and removed 21 (15 requested) atoms. Cycle 20: After refmac, R = 0.2763 (Rfree = 0.000) for 3343 atoms. Found 15 (27 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 3432 seeds are put forward NCS extension: 46 residues added (1 deleted due to clashes), 3478 seeds are put forward Round 1: 278 peptides, 39 chains. Longest chain 24 peptides. Score 0.524 Round 2: 300 peptides, 35 chains. Longest chain 25 peptides. Score 0.612 Round 3: 320 peptides, 36 chains. Longest chain 36 peptides. Score 0.642 Round 4: 305 peptides, 31 chains. Longest chain 45 peptides. Score 0.658 Round 5: 300 peptides, 34 chains. Longest chain 29 peptides. Score 0.621 Taking the results from Round 4 Chains 32, Residues 274, Estimated correctness of the model 55.7 % 2 chains (59 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6608 restraints for refining 3418 atoms. 5262 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2747 (Rfree = 0.000) for 3418 atoms. Found 27 (27 requested) and removed 23 (15 requested) atoms. Cycle 22: After refmac, R = 0.2687 (Rfree = 0.000) for 3400 atoms. Found 19 (27 requested) and removed 22 (15 requested) atoms. Cycle 23: After refmac, R = 0.2692 (Rfree = 0.000) for 3383 atoms. Found 24 (27 requested) and removed 16 (15 requested) atoms. Cycle 24: After refmac, R = 0.2707 (Rfree = 0.000) for 3377 atoms. Found 27 (27 requested) and removed 20 (15 requested) atoms. Cycle 25: After refmac, R = 0.2567 (Rfree = 0.000) for 3361 atoms. Found 16 (27 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.93 Search for helices and strands: 0 residues in 0 chains, 3453 seeds are put forward NCS extension: 30 residues added (12 deleted due to clashes), 3483 seeds are put forward Round 1: 272 peptides, 33 chains. Longest chain 27 peptides. Score 0.572 Round 2: 296 peptides, 34 chains. Longest chain 30 peptides. Score 0.613 Round 3: 319 peptides, 31 chains. Longest chain 28 peptides. Score 0.683 Round 4: 320 peptides, 30 chains. Longest chain 25 peptides. Score 0.693 Round 5: 315 peptides, 33 chains. Longest chain 25 peptides. Score 0.659 Taking the results from Round 4 Chains 34, Residues 290, Estimated correctness of the model 63.7 % 6 chains (103 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6085 restraints for refining 3418 atoms. 4491 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2759 (Rfree = 0.000) for 3418 atoms. Found 27 (27 requested) and removed 37 (15 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2738 (Rfree = 0.000) for 3395 atoms. Found 14 (27 requested) and removed 20 (15 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2647 (Rfree = 0.000) for 3382 atoms. Found 7 (27 requested) and removed 21 (15 requested) atoms. Cycle 29: After refmac, R = 0.2597 (Rfree = 0.000) for 3360 atoms. Found 12 (27 requested) and removed 18 (15 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2735 (Rfree = 0.000) for 3346 atoms. Found 27 (27 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 3431 seeds are put forward NCS extension: 32 residues added (10 deleted due to clashes), 3463 seeds are put forward Round 1: 250 peptides, 37 chains. Longest chain 22 peptides. Score 0.477 Round 2: 283 peptides, 33 chains. Longest chain 34 peptides. Score 0.596 Round 3: 284 peptides, 35 chains. Longest chain 35 peptides. Score 0.579 Round 4: 276 peptides, 35 chains. Longest chain 22 peptides. Score 0.561 Round 5: 283 peptides, 36 chains. Longest chain 27 peptides. Score 0.566 Taking the results from Round 2 Chains 34, Residues 250, Estimated correctness of the model 40.0 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9974 reflections ( 99.81 % complete ) and 6637 restraints for refining 3418 atoms. 5328 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2607 (Rfree = 0.000) for 3418 atoms. Found 27 (27 requested) and removed 38 (15 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2550 (Rfree = 0.000) for 3387 atoms. Found 23 (27 requested) and removed 22 (15 requested) atoms. Cycle 33: After refmac, R = 0.2535 (Rfree = 0.000) for 3376 atoms. Found 27 (27 requested) and removed 19 (15 requested) atoms. Cycle 34: After refmac, R = 0.2464 (Rfree = 0.000) for 3371 atoms. Found 19 (27 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.2456 (Rfree = 0.000) for 3369 atoms. Found 27 (27 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.93 Search for helices and strands: 0 residues in 0 chains, 3455 seeds are put forward NCS extension: 29 residues added (14 deleted due to clashes), 3484 seeds are put forward Round 1: 249 peptides, 33 chains. Longest chain 27 peptides. Score 0.519 Round 2: 307 peptides, 38 chains. Longest chain 26 peptides. Score 0.598 Round 3: 292 peptides, 36 chains. Longest chain 19 peptides. Score 0.586 Round 4: 304 peptides, 37 chains. Longest chain 41 peptides. Score 0.602 Round 5: 285 peptides, 35 chains. Longest chain 23 peptides. Score 0.581 Taking the results from Round 4 Chains 39, Residues 267, Estimated correctness of the model 41.6 % 5 chains (76 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6527 restraints for refining 3418 atoms. 5179 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2682 (Rfree = 0.000) for 3418 atoms. Found 21 (27 requested) and removed 24 (15 requested) atoms. Cycle 37: After refmac, R = 0.2661 (Rfree = 0.000) for 3391 atoms. Found 27 (27 requested) and removed 22 (15 requested) atoms. Cycle 38: After refmac, R = 0.2606 (Rfree = 0.000) for 3386 atoms. Found 22 (27 requested) and removed 20 (15 requested) atoms. Cycle 39: After refmac, R = 0.2616 (Rfree = 0.000) for 3372 atoms. Found 27 (27 requested) and removed 18 (15 requested) atoms. Cycle 40: After refmac, R = 0.2529 (Rfree = 0.000) for 3374 atoms. Found 19 (27 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.96 Search for helices and strands: 0 residues in 0 chains, 3438 seeds are put forward NCS extension: 46 residues added (19 deleted due to clashes), 3484 seeds are put forward Round 1: 233 peptides, 36 chains. Longest chain 16 peptides. Score 0.444 Round 2: 280 peptides, 33 chains. Longest chain 41 peptides. Score 0.590 Round 3: 278 peptides, 33 chains. Longest chain 23 peptides. Score 0.585 Round 4: 290 peptides, 35 chains. Longest chain 28 peptides. Score 0.591 Round 5: 290 peptides, 32 chains. Longest chain 32 peptides. Score 0.620 Taking the results from Round 5 Chains 32, Residues 258, Estimated correctness of the model 46.3 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6991 restraints for refining 3418 atoms. 5848 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2659 (Rfree = 0.000) for 3418 atoms. Found 24 (27 requested) and removed 21 (15 requested) atoms. Cycle 42: After refmac, R = 0.2619 (Rfree = 0.000) for 3407 atoms. Found 27 (27 requested) and removed 16 (15 requested) atoms. Cycle 43: After refmac, R = 0.2500 (Rfree = 0.000) for 3409 atoms. Found 27 (27 requested) and removed 18 (15 requested) atoms. Cycle 44: After refmac, R = 0.2546 (Rfree = 0.000) for 3405 atoms. Found 27 (27 requested) and removed 19 (15 requested) atoms. Cycle 45: After refmac, R = 0.2543 (Rfree = 0.000) for 3403 atoms. Found 27 (27 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 3508 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3523 seeds are put forward Round 1: 245 peptides, 41 chains. Longest chain 16 peptides. Score 0.417 Round 2: 260 peptides, 33 chains. Longest chain 23 peptides. Score 0.545 Round 3: 295 peptides, 34 chains. Longest chain 25 peptides. Score 0.611 Round 4: 285 peptides, 36 chains. Longest chain 22 peptides. Score 0.571 Round 5: 271 peptides, 32 chains. Longest chain 25 peptides. Score 0.580 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 261, Estimated correctness of the model 44.0 % 3 chains (47 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 1z85-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (261 residues) following loop building 3 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9974 reflections ( 99.81 % complete ) and 6731 restraints for refining 3418 atoms. 5501 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2696 (Rfree = 0.000) for 3418 atoms. Found 0 (27 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2635 (Rfree = 0.000) for 3383 atoms. Found 0 (27 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2633 (Rfree = 0.000) for 3357 atoms. Found 0 (27 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2574 (Rfree = 0.000) for 3334 atoms. Found 0 (26 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 63.4