Mon 24 Dec 00:57:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2itb-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:57:06 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/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-4.0-parrot-mrncs/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 221 and 0 Target number of residues in the AU: 221 Target solvent content: 0.6695 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-4.0-parrot-mrncs.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: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3296 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: 53.913 4.000 Wilson plot Bfac: 92.15 3315 reflections ( 99.55 % complete ) and 0 restraints for refining 3633 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3635 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3336 (Rfree = 0.000) for 3633 atoms. Found 9 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.04 4.76 Search for helices and strands: 0 residues in 0 chains, 3722 seeds are put forward NCS extension: 0 residues added, 3722 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 7 peptides. Score 0.233 Round 2: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.288 Round 3: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.308 Round 4: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.294 Round 5: 128 peptides, 22 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 5 Chains 22, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 7169 restraints for refining 2869 atoms. 6767 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3003 (Rfree = 0.000) for 2869 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.2787 (Rfree = 0.000) for 2850 atoms. Found 3 (13 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2682 (Rfree = 0.000) for 2834 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2677 (Rfree = 0.000) for 2827 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2632 (Rfree = 0.000) for 2821 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.93 4.63 Search for helices and strands: 0 residues in 0 chains, 2968 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 2979 seeds are put forward Round 1: 117 peptides, 23 chains. Longest chain 9 peptides. Score 0.300 Round 2: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.368 Round 3: 137 peptides, 21 chains. Longest chain 17 peptides. Score 0.434 Round 4: 141 peptides, 22 chains. Longest chain 13 peptides. Score 0.432 Round 5: 138 peptides, 21 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 5 Chains 21, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6578 restraints for refining 2692 atoms. 6131 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2976 (Rfree = 0.000) for 2692 atoms. Found 5 (12 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.2834 (Rfree = 0.000) for 2677 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 8: After refmac, R = 0.2757 (Rfree = 0.000) for 2670 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2733 (Rfree = 0.000) for 2663 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2688 (Rfree = 0.000) for 2654 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2778 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2798 seeds are put forward Round 1: 134 peptides, 27 chains. Longest chain 10 peptides. Score 0.301 Round 2: 148 peptides, 25 chains. Longest chain 12 peptides. Score 0.406 Round 3: 145 peptides, 22 chains. Longest chain 14 peptides. Score 0.449 Round 4: 148 peptides, 24 chains. Longest chain 12 peptides. Score 0.425 Round 5: 141 peptides, 24 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 3 Chains 22, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6687 restraints for refining 2758 atoms. 6217 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2859 (Rfree = 0.000) for 2758 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2695 (Rfree = 0.000) for 2752 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2625 (Rfree = 0.000) for 2745 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.2584 (Rfree = 0.000) for 2735 atoms. Found 0 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2561 (Rfree = 0.000) for 2725 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.94 4.64 Search for helices and strands: 0 residues in 0 chains, 2857 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2877 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 8 peptides. Score 0.282 Round 2: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.360 Round 3: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.385 Round 4: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.390 Round 5: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 5 Chains 23, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6886 restraints for refining 2794 atoms. 6449 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2780 (Rfree = 0.000) for 2794 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2640 (Rfree = 0.000) for 2794 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2553 (Rfree = 0.000) for 2785 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2579 (Rfree = 0.000) for 2778 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2530 (Rfree = 0.000) for 2772 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2916 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2928 seeds are put forward Round 1: 121 peptides, 24 chains. Longest chain 10 peptides. Score 0.299 Round 2: 130 peptides, 23 chains. Longest chain 11 peptides. Score 0.363 Round 3: 143 peptides, 25 chains. Longest chain 14 peptides. Score 0.383 Round 4: 150 peptides, 23 chains. Longest chain 11 peptides. Score 0.452 Round 5: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 4 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 6835 restraints for refining 2828 atoms. 6350 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2726 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 22: After refmac, R = 0.2549 (Rfree = 0.000) for 2824 atoms. Found 4 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2516 (Rfree = 0.000) for 2816 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2527 (Rfree = 0.000) for 2807 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2476 (Rfree = 0.000) for 2802 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.96 4.66 Search for helices and strands: 0 residues in 0 chains, 2931 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2934 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 8 peptides. Score 0.297 Round 2: 123 peptides, 21 chains. Longest chain 12 peptides. Score 0.371 Round 3: 116 peptides, 19 chains. Longest chain 11 peptides. Score 0.379 Round 4: 122 peptides, 21 chains. Longest chain 9 peptides. Score 0.366 Round 5: 119 peptides, 18 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3315 reflections ( 99.55 % complete ) and 6988 restraints for refining 2828 atoms. 6602 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2807 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 27: After refmac, R = 0.2580 (Rfree = 0.000) for 2827 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2561 (Rfree = 0.000) for 2819 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2513 (Rfree = 0.000) for 2815 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2526 (Rfree = 0.000) for 2809 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2959 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 9 peptides. Score 0.260 Round 2: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.315 Round 3: 121 peptides, 22 chains. Longest chain 11 peptides. Score 0.341 Round 4: 126 peptides, 25 chains. Longest chain 10 peptides. Score 0.303 Round 5: 130 peptides, 24 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 5 Chains 24, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 7119 restraints for refining 2859 atoms. 6719 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2644 (Rfree = 0.000) for 2859 atoms. Found 5 (13 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2496 (Rfree = 0.000) for 2845 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2458 (Rfree = 0.000) for 2835 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2448 (Rfree = 0.000) for 2828 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2446 (Rfree = 0.000) for 2820 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 4.63 Search for helices and strands: 0 residues in 0 chains, 2933 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2936 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 10 peptides. Score 0.250 Round 2: 113 peptides, 24 chains. Longest chain 7 peptides. Score 0.259 Round 3: 121 peptides, 25 chains. Longest chain 7 peptides. Score 0.278 Round 4: 125 peptides, 26 chains. Longest chain 7 peptides. Score 0.277 Round 5: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.330 Taking the results from Round 5 Chains 23, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 7072 restraints for refining 2847 atoms. 6695 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2567 (Rfree = 0.000) for 2847 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2405 (Rfree = 0.000) for 2840 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2385 (Rfree = 0.000) for 2828 atoms. Found 0 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2388 (Rfree = 0.000) for 2821 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2404 (Rfree = 0.000) for 2813 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.91 4.60 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 0 residues added, 2946 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 9 peptides. Score 0.221 Round 2: 95 peptides, 20 chains. Longest chain 9 peptides. Score 0.252 Round 3: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.280 Round 4: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.303 Round 5: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.320 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3315 reflections ( 99.55 % complete ) and 7054 restraints for refining 2833 atoms. 6759 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2525 (Rfree = 0.000) for 2833 atoms. Found 5 (13 requested) and removed 18 (6 requested) atoms. Cycle 42: After refmac, R = 0.2389 (Rfree = 0.000) for 2818 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2428 (Rfree = 0.000) for 2810 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2387 (Rfree = 0.000) for 2808 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2358 (Rfree = 0.000) for 2801 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.95 4.65 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 0 residues added, 2944 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.212 Round 2: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.266 Round 3: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.315 Round 4: 90 peptides, 15 chains. Longest chain 10 peptides. Score 0.340 Round 5: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.306 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 75, 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 2itb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3315 reflections ( 99.55 % complete ) and 6982 restraints for refining 2784 atoms. 6697 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2485 (Rfree = 0.000) for 2784 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2373 (Rfree = 0.000) for 2777 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2345 (Rfree = 0.000) for 2768 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2321 (Rfree = 0.000) for 2760 atoms. TimeTaking 34.85