Sun 23 Dec 22:23:05 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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/2hxv-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 ============================================================ Sun 23 Dec 22:23:14 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-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 267 and 0 Target number of residues in the AU: 267 Target solvent content: 0.6373 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-3.2-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: 97 Cell parameters: 104.410 104.410 146.200 90.000 90.000 90.000 Input sequence file: 2hxv-3.2-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 3.200 Wilson plot Bfac: 70.03 6960 reflections ( 99.59 % complete ) and 0 restraints for refining 3188 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3504 (Rfree = 0.000) for 3188 atoms. Found 28 (28 requested) and removed 45 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3206 seeds are put forward Round 1: 137 peptides, 28 chains. Longest chain 8 peptides. Score 0.286 Round 2: 202 peptides, 34 chains. Longest chain 13 peptides. Score 0.449 Round 3: 214 peptides, 33 chains. Longest chain 13 peptides. Score 0.507 Round 4: 225 peptides, 34 chains. Longest chain 16 peptides. Score 0.530 Round 5: 230 peptides, 31 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 5 Chains 32, Residues 199, Estimated correctness of the model 37.8 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5568 restraints for refining 2629 atoms. 4770 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3071 (Rfree = 0.000) for 2629 atoms. Found 18 (23 requested) and removed 34 (11 requested) atoms. Cycle 2: After refmac, R = 0.3223 (Rfree = 0.000) for 2567 atoms. Found 17 (23 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2778 (Rfree = 0.000) for 2549 atoms. Found 14 (22 requested) and removed 22 (11 requested) atoms. Cycle 4: After refmac, R = 0.2902 (Rfree = 0.000) for 2529 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2620 (Rfree = 0.000) for 2525 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 2582 seeds are put forward Round 1: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.464 Round 2: 218 peptides, 29 chains. Longest chain 20 peptides. Score 0.578 Round 3: 228 peptides, 29 chains. Longest chain 21 peptides. Score 0.608 Round 4: 223 peptides, 30 chains. Longest chain 16 peptides. Score 0.580 Round 5: 224 peptides, 27 chains. Longest chain 20 peptides. Score 0.623 Taking the results from Round 5 Chains 27, Residues 197, Estimated correctness of the model 47.1 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5617 restraints for refining 2629 atoms. 4773 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2739 (Rfree = 0.000) for 2629 atoms. Found 14 (23 requested) and removed 22 (11 requested) atoms. Cycle 7: After refmac, R = 0.2599 (Rfree = 0.000) for 2613 atoms. Found 13 (23 requested) and removed 22 (11 requested) atoms. Cycle 8: After refmac, R = 0.2433 (Rfree = 0.000) for 2597 atoms. Found 8 (23 requested) and removed 12 (11 requested) atoms. Cycle 9: After refmac, R = 0.2438 (Rfree = 0.000) for 2589 atoms. Found 7 (23 requested) and removed 24 (11 requested) atoms. Cycle 10: After refmac, R = 0.2811 (Rfree = 0.000) for 2566 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 2640 seeds are put forward Round 1: 188 peptides, 29 chains. Longest chain 15 peptides. Score 0.477 Round 2: 223 peptides, 30 chains. Longest chain 18 peptides. Score 0.580 Round 3: 221 peptides, 29 chains. Longest chain 17 peptides. Score 0.587 Round 4: 219 peptides, 29 chains. Longest chain 20 peptides. Score 0.581 Round 5: 212 peptides, 25 chains. Longest chain 20 peptides. Score 0.615 Taking the results from Round 5 Chains 26, Residues 187, Estimated correctness of the model 45.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5630 restraints for refining 2628 atoms. 4837 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2902 (Rfree = 0.000) for 2628 atoms. Found 21 (23 requested) and removed 21 (11 requested) atoms. Cycle 12: After refmac, R = 0.2497 (Rfree = 0.000) for 2619 atoms. Found 9 (23 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2570 (Rfree = 0.000) for 2605 atoms. Found 19 (23 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2493 (Rfree = 0.000) for 2602 atoms. Found 13 (23 requested) and removed 16 (11 requested) atoms. Cycle 15: After refmac, R = 0.2502 (Rfree = 0.000) for 2594 atoms. Found 16 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 2659 seeds are put forward Round 1: 191 peptides, 33 chains. Longest chain 13 peptides. Score 0.423 Round 2: 206 peptides, 32 chains. Longest chain 22 peptides. Score 0.495 Round 3: 195 peptides, 28 chains. Longest chain 16 peptides. Score 0.517 Round 4: 213 peptides, 31 chains. Longest chain 15 peptides. Score 0.534 Round 5: 233 peptides, 34 chains. Longest chain 16 peptides. Score 0.556 Taking the results from Round 5 Chains 34, Residues 199, Estimated correctness of the model 28.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5701 restraints for refining 2627 atoms. 4939 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2727 (Rfree = 0.000) for 2627 atoms. Found 21 (23 requested) and removed 13 (11 requested) atoms. Cycle 17: After refmac, R = 0.2654 (Rfree = 0.000) for 2628 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.2672 (Rfree = 0.000) for 2612 atoms. Found 17 (23 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.2739 (Rfree = 0.000) for 2608 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.2602 (Rfree = 0.000) for 2611 atoms. Found 16 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 2687 seeds are put forward Round 1: 165 peptides, 30 chains. Longest chain 9 peptides. Score 0.371 Round 2: 190 peptides, 30 chains. Longest chain 13 peptides. Score 0.468 Round 3: 202 peptides, 30 chains. Longest chain 12 peptides. Score 0.511 Round 4: 205 peptides, 26 chains. Longest chain 18 peptides. Score 0.580 Round 5: 190 peptides, 28 chains. Longest chain 14 peptides. Score 0.500 Taking the results from Round 4 Chains 27, Residues 179, Estimated correctness of the model 35.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5677 restraints for refining 2629 atoms. 4936 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2792 (Rfree = 0.000) for 2629 atoms. Found 9 (23 requested) and removed 15 (11 requested) atoms. Cycle 22: After refmac, R = 0.2912 (Rfree = 0.000) for 2607 atoms. Found 21 (23 requested) and removed 16 (11 requested) atoms. Cycle 23: After refmac, R = 0.2804 (Rfree = 0.000) for 2611 atoms. Found 12 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.2541 (Rfree = 0.000) for 2607 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.2478 (Rfree = 0.000) for 2590 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 2655 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 13 peptides. Score 0.351 Round 2: 178 peptides, 26 chains. Longest chain 15 peptides. Score 0.489 Round 3: 189 peptides, 26 chains. Longest chain 19 peptides. Score 0.527 Round 4: 205 peptides, 26 chains. Longest chain 17 peptides. Score 0.580 Round 5: 208 peptides, 29 chains. Longest chain 21 peptides. Score 0.546 Taking the results from Round 4 Chains 27, Residues 179, Estimated correctness of the model 35.6 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5622 restraints for refining 2627 atoms. 4860 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2681 (Rfree = 0.000) for 2627 atoms. Found 8 (23 requested) and removed 16 (11 requested) atoms. Cycle 27: After refmac, R = 0.2572 (Rfree = 0.000) for 2608 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.2622 (Rfree = 0.000) for 2598 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.3063 (Rfree = 0.000) for 2590 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 30: After refmac, R = 0.2984 (Rfree = 0.000) for 2594 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 2662 seeds are put forward Round 1: 160 peptides, 31 chains. Longest chain 10 peptides. Score 0.332 Round 2: 191 peptides, 29 chains. Longest chain 12 peptides. Score 0.488 Round 3: 177 peptides, 24 chains. Longest chain 16 peptides. Score 0.517 Round 4: 182 peptides, 24 chains. Longest chain 21 peptides. Score 0.534 Round 5: 186 peptides, 26 chains. Longest chain 16 peptides. Score 0.517 Taking the results from Round 4 Chains 24, Residues 158, Estimated correctness of the model 22.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5915 restraints for refining 2629 atoms. 5307 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2838 (Rfree = 0.000) for 2629 atoms. Found 19 (23 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.2793 (Rfree = 0.000) for 2619 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 33: After refmac, R = 0.2707 (Rfree = 0.000) for 2607 atoms. Found 19 (23 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.2699 (Rfree = 0.000) for 2613 atoms. Found 22 (23 requested) and removed 20 (11 requested) atoms. Cycle 35: After refmac, R = 0.2689 (Rfree = 0.000) for 2609 atoms. Found 23 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 2679 seeds are put forward Round 1: 146 peptides, 29 chains. Longest chain 8 peptides. Score 0.308 Round 2: 172 peptides, 27 chains. Longest chain 17 peptides. Score 0.450 Round 3: 165 peptides, 26 chains. Longest chain 15 peptides. Score 0.440 Round 4: 162 peptides, 25 chains. Longest chain 13 peptides. Score 0.445 Round 5: 170 peptides, 27 chains. Longest chain 18 peptides. Score 0.442 Taking the results from Round 2 Chains 27, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5964 restraints for refining 2629 atoms. 5411 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2614 (Rfree = 0.000) for 2629 atoms. Found 12 (23 requested) and removed 11 (11 requested) atoms. Cycle 37: After refmac, R = 0.2587 (Rfree = 0.000) for 2624 atoms. Found 16 (23 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.2226 (Rfree = 0.000) for 2624 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2317 (Rfree = 0.000) for 2615 atoms. Found 20 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.2091 (Rfree = 0.000) for 2615 atoms. Found 7 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 2632 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 10 peptides. Score 0.280 Round 2: 157 peptides, 27 chains. Longest chain 17 peptides. Score 0.391 Round 3: 164 peptides, 25 chains. Longest chain 12 peptides. Score 0.453 Round 4: 157 peptides, 24 chains. Longest chain 17 peptides. Score 0.443 Round 5: 156 peptides, 25 chains. Longest chain 17 peptides. Score 0.422 Taking the results from Round 3 Chains 25, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6960 reflections ( 99.59 % complete ) and 5747 restraints for refining 2613 atoms. 5216 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2581 (Rfree = 0.000) for 2613 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 42: After refmac, R = 0.2548 (Rfree = 0.000) for 2604 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 43: After refmac, R = 0.2409 (Rfree = 0.000) for 2609 atoms. Found 22 (23 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.2640 (Rfree = 0.000) for 2616 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 45: After refmac, R = 0.2403 (Rfree = 0.000) for 2612 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 2655 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.311 Round 2: 153 peptides, 26 chains. Longest chain 11 peptides. Score 0.392 Round 3: 156 peptides, 24 chains. Longest chain 13 peptides. Score 0.439 Round 4: 154 peptides, 25 chains. Longest chain 13 peptides. Score 0.414 Round 5: 152 peptides, 22 chains. Longest chain 15 peptides. Score 0.458 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 130, 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. 6960 reflections ( 99.59 % complete ) and 5902 restraints for refining 2629 atoms. 5404 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2578 (Rfree = 0.000) for 2629 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2393 (Rfree = 0.000) for 2612 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2203 (Rfree = 0.000) for 2594 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2139 (Rfree = 0.000) for 2582 atoms. TimeTaking 53.5