null Sun 23 Dec 22:22:43 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 2hxv-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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/2hxv-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 22:22:52 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/2hxv-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 264 and 0 Target number of residues in the AU: 264 Target solvent content: 0.6414 Checking the provided sequence file Detected sequence length: 360 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 360 Adjusted target solvent content: 0.51 Input MTZ file: 2hxv-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: 97 Cell parameters: 104.410 104.410 146.200 90.000 90.000 90.000 Input sequence file: 2hxv-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2880 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 Loops will be built when appropriate and at the last cycle Resolution range: 84.967 3.400 Wilson plot Bfac: 72.65 5830 reflections ( 99.52 % complete ) and 0 restraints for refining 3198 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3373 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3256 (Rfree = 0.000) for 3198 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 3258 seeds are put forward Round 1: 169 peptides, 32 chains. Longest chain 12 peptides. Score 0.352 Round 2: 214 peptides, 34 chains. Longest chain 17 peptides. Score 0.492 Round 3: 227 peptides, 32 chains. Longest chain 17 peptides. Score 0.565 Round 4: 230 peptides, 30 chains. Longest chain 23 peptides. Score 0.601 Round 5: 237 peptides, 28 chains. Longest chain 22 peptides. Score 0.646 Taking the results from Round 5 Chains 29, Residues 209, Estimated correctness of the model 43.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5568 restraints for refining 2619 atoms. 4693 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2878 (Rfree = 0.000) for 2619 atoms. Found 17 (19 requested) and removed 39 (9 requested) atoms. Cycle 2: After refmac, R = 0.2698 (Rfree = 0.000) for 2554 atoms. Found 10 (19 requested) and removed 33 (9 requested) atoms. Cycle 3: After refmac, R = 0.2779 (Rfree = 0.000) for 2513 atoms. Found 9 (19 requested) and removed 20 (9 requested) atoms. Cycle 4: After refmac, R = 0.2517 (Rfree = 0.000) for 2490 atoms. Found 5 (18 requested) and removed 16 (9 requested) atoms. Cycle 5: After refmac, R = 0.2494 (Rfree = 0.000) for 2473 atoms. Found 6 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 2516 seeds are put forward Round 1: 201 peptides, 33 chains. Longest chain 16 peptides. Score 0.461 Round 2: 237 peptides, 36 chains. Longest chain 16 peptides. Score 0.541 Round 3: 218 peptides, 32 chains. Longest chain 28 peptides. Score 0.536 Round 4: 230 peptides, 32 chains. Longest chain 27 peptides. Score 0.574 Round 5: 230 peptides, 32 chains. Longest chain 23 peptides. Score 0.574 Taking the results from Round 5 Chains 32, Residues 198, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5838 restraints for refining 2595 atoms. 5078 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2697 (Rfree = 0.000) for 2595 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2627 (Rfree = 0.000) for 2581 atoms. Found 17 (19 requested) and removed 15 (9 requested) atoms. Cycle 8: After refmac, R = 0.2573 (Rfree = 0.000) for 2570 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.2493 (Rfree = 0.000) for 2549 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.2590 (Rfree = 0.000) for 2544 atoms. Found 14 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 2610 seeds are put forward Round 1: 200 peptides, 35 chains. Longest chain 10 peptides. Score 0.425 Round 2: 231 peptides, 34 chains. Longest chain 22 peptides. Score 0.550 Round 3: 235 peptides, 31 chains. Longest chain 22 peptides. Score 0.603 Round 4: 233 peptides, 34 chains. Longest chain 17 peptides. Score 0.556 Round 5: 240 peptides, 29 chains. Longest chain 21 peptides. Score 0.642 Taking the results from Round 5 Chains 30, Residues 211, Estimated correctness of the model 41.8 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5440 restraints for refining 2596 atoms. 4534 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2739 (Rfree = 0.000) for 2596 atoms. Found 12 (19 requested) and removed 34 (9 requested) atoms. Cycle 12: After refmac, R = 0.2563 (Rfree = 0.000) for 2561 atoms. Found 13 (19 requested) and removed 21 (9 requested) atoms. Cycle 13: After refmac, R = 0.2479 (Rfree = 0.000) for 2539 atoms. Found 11 (19 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.3084 (Rfree = 0.000) for 2526 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 15: After refmac, R = 0.2396 (Rfree = 0.000) for 2507 atoms. Found 13 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 2552 seeds are put forward Round 1: 203 peptides, 35 chains. Longest chain 15 peptides. Score 0.436 Round 2: 221 peptides, 34 chains. Longest chain 25 peptides. Score 0.517 Round 3: 234 peptides, 36 chains. Longest chain 27 peptides. Score 0.531 Round 4: 220 peptides, 33 chains. Longest chain 25 peptides. Score 0.528 Round 5: 221 peptides, 34 chains. Longest chain 19 peptides. Score 0.517 Taking the results from Round 3 Chains 37, Residues 198, Estimated correctness of the model 4.6 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5412 restraints for refining 2619 atoms. 4519 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2786 (Rfree = 0.000) for 2619 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 17: After refmac, R = 0.2769 (Rfree = 0.000) for 2609 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 18: After refmac, R = 0.2717 (Rfree = 0.000) for 2606 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 19: After refmac, R = 0.2635 (Rfree = 0.000) for 2601 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 20: After refmac, R = 0.2407 (Rfree = 0.000) for 2601 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 2653 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 14 peptides. Score 0.329 Round 2: 202 peptides, 32 chains. Longest chain 17 peptides. Score 0.480 Round 3: 189 peptides, 31 chains. Longest chain 15 peptides. Score 0.448 Round 4: 194 peptides, 30 chains. Longest chain 24 peptides. Score 0.483 Round 5: 201 peptides, 32 chains. Longest chain 20 peptides. Score 0.477 Taking the results from Round 4 Chains 30, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5833 restraints for refining 2618 atoms. 5207 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2771 (Rfree = 0.000) for 2618 atoms. Found 17 (19 requested) and removed 13 (9 requested) atoms. Cycle 22: After refmac, R = 0.2602 (Rfree = 0.000) for 2608 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 23: After refmac, R = 0.2546 (Rfree = 0.000) for 2603 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 24: After refmac, R = 0.2464 (Rfree = 0.000) for 2600 atoms. Found 17 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.2491 (Rfree = 0.000) for 2604 atoms. Found 18 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 2662 seeds are put forward Round 1: 187 peptides, 36 chains. Longest chain 24 peptides. Score 0.357 Round 2: 194 peptides, 34 chains. Longest chain 21 peptides. Score 0.418 Round 3: 195 peptides, 31 chains. Longest chain 21 peptides. Score 0.471 Round 4: 194 peptides, 31 chains. Longest chain 21 peptides. Score 0.467 Round 5: 193 peptides, 30 chains. Longest chain 21 peptides. Score 0.479 Taking the results from Round 5 Chains 30, Residues 163, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5759 restraints for refining 2619 atoms. 5100 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2443 (Rfree = 0.000) for 2619 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. Cycle 27: After refmac, R = 0.2329 (Rfree = 0.000) for 2610 atoms. Found 13 (19 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.2425 (Rfree = 0.000) for 2607 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 29: After refmac, R = 0.2317 (Rfree = 0.000) for 2602 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.2258 (Rfree = 0.000) for 2604 atoms. Found 15 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 2654 seeds are put forward Round 1: 176 peptides, 36 chains. Longest chain 13 peptides. Score 0.311 Round 2: 178 peptides, 30 chains. Longest chain 20 peptides. Score 0.423 Round 3: 204 peptides, 32 chains. Longest chain 21 peptides. Score 0.488 Round 4: 204 peptides, 28 chains. Longest chain 21 peptides. Score 0.548 Round 5: 189 peptides, 28 chains. Longest chain 22 peptides. Score 0.496 Taking the results from Round 4 Chains 30, Residues 176, Estimated correctness of the model 10.8 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5537 restraints for refining 2618 atoms. 4782 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2576 (Rfree = 0.000) for 2618 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 32: After refmac, R = 0.2355 (Rfree = 0.000) for 2606 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2316 (Rfree = 0.000) for 2607 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2290 (Rfree = 0.000) for 2595 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2496 (Rfree = 0.000) for 2586 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 2629 seeds are put forward Round 1: 174 peptides, 36 chains. Longest chain 12 peptides. Score 0.302 Round 2: 201 peptides, 34 chains. Longest chain 23 peptides. Score 0.445 Round 3: 218 peptides, 36 chains. Longest chain 12 peptides. Score 0.476 Round 4: 209 peptides, 33 chains. Longest chain 19 peptides. Score 0.490 Round 5: 207 peptides, 33 chains. Longest chain 20 peptides. Score 0.483 Taking the results from Round 4 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5853 restraints for refining 2619 atoms. 5182 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2528 (Rfree = 0.000) for 2619 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.2413 (Rfree = 0.000) for 2614 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.2374 (Rfree = 0.000) for 2612 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.2262 (Rfree = 0.000) for 2608 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2237 (Rfree = 0.000) for 2605 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 2644 seeds are put forward Round 1: 148 peptides, 27 chains. Longest chain 12 peptides. Score 0.353 Round 2: 165 peptides, 27 chains. Longest chain 17 peptides. Score 0.423 Round 3: 158 peptides, 24 chains. Longest chain 17 peptides. Score 0.447 Round 4: 149 peptides, 23 chains. Longest chain 15 peptides. Score 0.429 Round 5: 162 peptides, 25 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 3 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.52 % complete ) and 5865 restraints for refining 2619 atoms. 5280 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2433 (Rfree = 0.000) for 2619 atoms. Found 16 (19 requested) and removed 25 (9 requested) atoms. Cycle 42: After refmac, R = 0.2426 (Rfree = 0.000) for 2608 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2314 (Rfree = 0.000) for 2595 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2802 (Rfree = 0.000) for 2584 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.2528 (Rfree = 0.000) for 2587 atoms. Found 17 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 2627 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 12 peptides. Score 0.250 Round 2: 158 peptides, 28 chains. Longest chain 14 peptides. Score 0.377 Round 3: 162 peptides, 29 chains. Longest chain 15 peptides. Score 0.376 Round 4: 168 peptides, 30 chains. Longest chain 14 peptides. Score 0.383 Round 5: 177 peptides, 30 chains. Longest chain 15 peptides. Score 0.419 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 147, 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 2hxv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5830 reflections ( 99.52 % complete ) and 5950 restraints for refining 2619 atoms. 5392 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2467 (Rfree = 0.000) for 2619 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2455 (Rfree = 0.000) for 2607 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2439 (Rfree = 0.000) for 2594 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2357 (Rfree = 0.000) for 2583 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:27 GMT 2018 Job finished. TimeTaking 51.74 Used memory is bytes: 14971056