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 1vli-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vli-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-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/1vli-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-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 22:22:53 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/1vli-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-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 383 and 0 Target number of residues in the AU: 383 Target solvent content: 0.6495 Checking the provided sequence file Detected sequence length: 385 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 385 Adjusted target solvent content: 0.65 Input MTZ file: 1vli-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: 154 Cell parameters: 70.614 70.614 205.438 90.000 90.000 120.000 Input sequence file: 1vli-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3080 target number of atoms Had to go as low as 1.05 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: 68.479 3.201 Wilson plot Bfac: 77.85 10359 reflections ( 99.78 % complete ) and 0 restraints for refining 3454 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Starting model: R = 0.3674 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3312 (Rfree = 0.000) for 3454 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3525 seeds are put forward Round 1: 205 peptides, 31 chains. Longest chain 14 peptides. Score 0.423 Round 2: 245 peptides, 30 chains. Longest chain 18 peptides. Score 0.535 Round 3: 251 peptides, 25 chains. Longest chain 22 peptides. Score 0.600 Round 4: 250 peptides, 26 chains. Longest chain 21 peptides. Score 0.588 Round 5: 252 peptides, 25 chains. Longest chain 32 peptides. Score 0.602 Taking the results from Round 5 Chains 27, Residues 227, Estimated correctness of the model 41.5 % 4 chains (65 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5561 restraints for refining 2810 atoms. 4424 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2987 (Rfree = 0.000) for 2810 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 2: After refmac, R = 0.2846 (Rfree = 0.000) for 2766 atoms. Found 21 (25 requested) and removed 13 (12 requested) atoms. Cycle 3: After refmac, R = 0.2861 (Rfree = 0.000) for 2752 atoms. Found 19 (24 requested) and removed 15 (12 requested) atoms. Cycle 4: After refmac, R = 0.2593 (Rfree = 0.000) for 2734 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. Cycle 5: After refmac, R = 0.2679 (Rfree = 0.000) for 2719 atoms. Found 17 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 2834 seeds are put forward Round 1: 228 peptides, 30 chains. Longest chain 19 peptides. Score 0.495 Round 2: 251 peptides, 24 chains. Longest chain 24 peptides. Score 0.610 Round 3: 262 peptides, 25 chains. Longest chain 27 peptides. Score 0.623 Round 4: 263 peptides, 24 chains. Longest chain 30 peptides. Score 0.634 Round 5: 255 peptides, 21 chains. Longest chain 22 peptides. Score 0.647 Taking the results from Round 5 Chains 23, Residues 234, Estimated correctness of the model 53.1 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5905 restraints for refining 2811 atoms. 4882 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2884 (Rfree = 0.000) for 2811 atoms. Found 22 (25 requested) and removed 14 (12 requested) atoms. Cycle 7: After refmac, R = 0.2805 (Rfree = 0.000) for 2790 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 8: After refmac, R = 0.2657 (Rfree = 0.000) for 2781 atoms. Found 13 (25 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2567 (Rfree = 0.000) for 2769 atoms. Found 13 (24 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2384 (Rfree = 0.000) for 2763 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 2902 seeds are put forward Round 1: 256 peptides, 30 chains. Longest chain 22 peptides. Score 0.560 Round 2: 267 peptides, 25 chains. Longest chain 34 peptides. Score 0.632 Round 3: 268 peptides, 26 chains. Longest chain 26 peptides. Score 0.625 Round 4: 276 peptides, 26 chains. Longest chain 31 peptides. Score 0.640 Round 5: 281 peptides, 28 chains. Longest chain 25 peptides. Score 0.632 Taking the results from Round 4 Chains 29, Residues 250, Estimated correctness of the model 51.3 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5468 restraints for refining 2812 atoms. 4297 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2762 (Rfree = 0.000) for 2812 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 12: After refmac, R = 0.2677 (Rfree = 0.000) for 2809 atoms. Found 15 (25 requested) and removed 15 (12 requested) atoms. Cycle 13: After refmac, R = 0.2534 (Rfree = 0.000) for 2802 atoms. Found 17 (25 requested) and removed 18 (12 requested) atoms. Cycle 14: After refmac, R = 0.2595 (Rfree = 0.000) for 2794 atoms. Found 16 (25 requested) and removed 16 (12 requested) atoms. Cycle 15: After refmac, R = 0.2384 (Rfree = 0.000) for 2790 atoms. Found 15 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.73 Search for helices and strands: 0 residues in 0 chains, 2891 seeds are put forward Round 1: 254 peptides, 28 chains. Longest chain 23 peptides. Score 0.576 Round 2: 268 peptides, 26 chains. Longest chain 27 peptides. Score 0.625 Round 3: 278 peptides, 29 chains. Longest chain 23 peptides. Score 0.617 Round 4: 266 peptides, 25 chains. Longest chain 26 peptides. Score 0.630 Round 5: 273 peptides, 26 chains. Longest chain 26 peptides. Score 0.635 Taking the results from Round 5 Chains 30, Residues 247, Estimated correctness of the model 50.1 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5402 restraints for refining 2811 atoms. 4242 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 2811 atoms. Found 25 (25 requested) and removed 15 (12 requested) atoms. Cycle 17: After refmac, R = 0.2754 (Rfree = 0.000) for 2799 atoms. Found 20 (25 requested) and removed 18 (12 requested) atoms. Cycle 18: After refmac, R = 0.2460 (Rfree = 0.000) for 2784 atoms. Found 15 (25 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.2415 (Rfree = 0.000) for 2784 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. Cycle 20: After refmac, R = 0.2665 (Rfree = 0.000) for 2769 atoms. Found 18 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.70 Search for helices and strands: 0 residues in 0 chains, 2871 seeds are put forward Round 1: 235 peptides, 31 chains. Longest chain 19 peptides. Score 0.501 Round 2: 265 peptides, 29 chains. Longest chain 20 peptides. Score 0.590 Round 3: 268 peptides, 27 chains. Longest chain 21 peptides. Score 0.616 Round 4: 248 peptides, 22 chains. Longest chain 32 peptides. Score 0.624 Round 5: 263 peptides, 26 chains. Longest chain 26 peptides. Score 0.615 Taking the results from Round 4 Chains 26, Residues 226, Estimated correctness of the model 47.3 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5714 restraints for refining 2811 atoms. 4661 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2711 (Rfree = 0.000) for 2811 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 22: After refmac, R = 0.2645 (Rfree = 0.000) for 2799 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 23: After refmac, R = 0.2532 (Rfree = 0.000) for 2791 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.2545 (Rfree = 0.000) for 2781 atoms. Found 15 (24 requested) and removed 16 (12 requested) atoms. Cycle 25: After refmac, R = 0.2929 (Rfree = 0.000) for 2773 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.71 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward Round 1: 226 peptides, 30 chains. Longest chain 14 peptides. Score 0.490 Round 2: 254 peptides, 30 chains. Longest chain 22 peptides. Score 0.556 Round 3: 269 peptides, 30 chains. Longest chain 22 peptides. Score 0.589 Round 4: 265 peptides, 24 chains. Longest chain 35 peptides. Score 0.638 Round 5: 270 peptides, 29 chains. Longest chain 28 peptides. Score 0.600 Taking the results from Round 4 Chains 24, Residues 241, Estimated correctness of the model 50.9 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5725 restraints for refining 2812 atoms. 4692 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2984 (Rfree = 0.000) for 2812 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 27: After refmac, R = 0.2507 (Rfree = 0.000) for 2797 atoms. Found 11 (25 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.2531 (Rfree = 0.000) for 2784 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.2463 (Rfree = 0.000) for 2774 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2850 (Rfree = 0.000) for 2765 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.75 Search for helices and strands: 0 residues in 0 chains, 2891 seeds are put forward Round 1: 226 peptides, 31 chains. Longest chain 20 peptides. Score 0.478 Round 2: 263 peptides, 27 chains. Longest chain 29 peptides. Score 0.605 Round 3: 268 peptides, 25 chains. Longest chain 31 peptides. Score 0.634 Round 4: 262 peptides, 24 chains. Longest chain 36 peptides. Score 0.632 Round 5: 264 peptides, 19 chains. Longest chain 29 peptides. Score 0.681 Taking the results from Round 5 Chains 22, Residues 245, Estimated correctness of the model 61.0 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5524 restraints for refining 2809 atoms. 4395 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2857 (Rfree = 0.000) for 2809 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 32: After refmac, R = 0.2778 (Rfree = 0.000) for 2803 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2590 (Rfree = 0.000) for 2798 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. Cycle 34: After refmac, R = 0.2542 (Rfree = 0.000) for 2792 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2729 (Rfree = 0.000) for 2781 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.74 Search for helices and strands: 0 residues in 0 chains, 2886 seeds are put forward Round 1: 239 peptides, 31 chains. Longest chain 16 peptides. Score 0.510 Round 2: 265 peptides, 25 chains. Longest chain 28 peptides. Score 0.628 Round 3: 276 peptides, 29 chains. Longest chain 39 peptides. Score 0.613 Round 4: 260 peptides, 25 chains. Longest chain 36 peptides. Score 0.619 Round 5: 275 peptides, 27 chains. Longest chain 26 peptides. Score 0.629 Taking the results from Round 5 Chains 30, Residues 248, Estimated correctness of the model 48.6 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5589 restraints for refining 2811 atoms. 4472 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2824 (Rfree = 0.000) for 2811 atoms. Found 23 (25 requested) and removed 17 (12 requested) atoms. Cycle 37: After refmac, R = 0.2658 (Rfree = 0.000) for 2804 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. Cycle 38: After refmac, R = 0.2516 (Rfree = 0.000) for 2797 atoms. Found 11 (25 requested) and removed 15 (12 requested) atoms. Cycle 39: After refmac, R = 0.2460 (Rfree = 0.000) for 2786 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2423 (Rfree = 0.000) for 2781 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 2.75 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward Round 1: 240 peptides, 30 chains. Longest chain 25 peptides. Score 0.524 Round 2: 250 peptides, 25 chains. Longest chain 36 peptides. Score 0.598 Round 3: 253 peptides, 25 chains. Longest chain 38 peptides. Score 0.604 Round 4: 262 peptides, 25 chains. Longest chain 34 peptides. Score 0.623 Round 5: 262 peptides, 28 chains. Longest chain 32 peptides. Score 0.594 Taking the results from Round 4 Chains 28, Residues 237, Estimated correctness of the model 47.1 % 2 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10359 reflections ( 99.78 % complete ) and 5615 restraints for refining 2812 atoms. 4529 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2686 (Rfree = 0.000) for 2812 atoms. Found 19 (25 requested) and removed 17 (12 requested) atoms. Cycle 42: After refmac, R = 0.2698 (Rfree = 0.000) for 2801 atoms. Found 25 (25 requested) and removed 15 (12 requested) atoms. Cycle 43: After refmac, R = 0.2525 (Rfree = 0.000) for 2802 atoms. Found 12 (25 requested) and removed 18 (12 requested) atoms. Cycle 44: After refmac, R = 0.2792 (Rfree = 0.000) for 2790 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. Cycle 45: After refmac, R = 0.2723 (Rfree = 0.000) for 2789 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.73 Search for helices and strands: 0 residues in 0 chains, 2891 seeds are put forward Round 1: 219 peptides, 31 chains. Longest chain 23 peptides. Score 0.460 Round 2: 246 peptides, 29 chains. Longest chain 24 peptides. Score 0.548 Round 3: 242 peptides, 28 chains. Longest chain 22 peptides. Score 0.550 Round 4: 239 peptides, 25 chains. Longest chain 23 peptides. Score 0.575 Round 5: 246 peptides, 32 chains. Longest chain 23 peptides. Score 0.516 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 214, Estimated correctness of the model 34.1 % 3 chains (36 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1vli-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (214 residues) following loop building 3 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10359 reflections ( 99.78 % complete ) and 5818 restraints for refining 2812 atoms. 4847 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2633 (Rfree = 0.000) for 2812 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2878 (Rfree = 0.000) for 2789 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2485 (Rfree = 0.000) for 2761 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2445 (Rfree = 0.000) for 2739 atoms. TimeTaking 58.13