Sun 23 Dec 23:57:11 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-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 ============================================================ Sun 23 Dec 23:57:15 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-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 241 and 0 Target number of residues in the AU: 241 Target solvent content: 0.6396 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-3.4-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-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.60 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 3.401 Wilson plot Bfac: 71.79 5306 reflections ( 99.72 % complete ) and 0 restraints for refining 3628 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3480 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3535 (Rfree = 0.000) for 3628 atoms. Found 19 (27 requested) and removed 34 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 0 residues added, 3721 seeds are put forward Round 1: 95 peptides, 22 chains. Longest chain 7 peptides. Score 0.207 Round 2: 126 peptides, 26 chains. Longest chain 8 peptides. Score 0.282 Round 3: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.337 Round 4: 155 peptides, 31 chains. Longest chain 11 peptides. Score 0.321 Round 5: 152 peptides, 29 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Chains 29, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7114 restraints for refining 2988 atoms. 6651 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2830 (Rfree = 0.000) for 2988 atoms. Found 21 (22 requested) and removed 21 (11 requested) atoms. Cycle 2: After refmac, R = 0.2646 (Rfree = 0.000) for 2949 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2542 (Rfree = 0.000) for 2933 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2519 (Rfree = 0.000) for 2922 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2495 (Rfree = 0.000) for 2910 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 3024 seeds are put forward NCS extension: 0 residues added, 3024 seeds are put forward Round 1: 124 peptides, 29 chains. Longest chain 6 peptides. Score 0.209 Round 2: 161 peptides, 31 chains. Longest chain 11 peptides. Score 0.349 Round 3: 173 peptides, 33 chains. Longest chain 12 peptides. Score 0.365 Round 4: 166 peptides, 30 chains. Longest chain 9 peptides. Score 0.390 Round 5: 184 peptides, 31 chains. Longest chain 10 peptides. Score 0.449 Taking the results from Round 5 Chains 31, Residues 153, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6395 restraints for refining 2768 atoms. 5791 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2912 (Rfree = 0.000) for 2768 atoms. Found 10 (20 requested) and removed 27 (10 requested) atoms. Cycle 7: After refmac, R = 0.2809 (Rfree = 0.000) for 2732 atoms. Found 5 (20 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.2720 (Rfree = 0.000) for 2717 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. Cycle 9: After refmac, R = 0.2760 (Rfree = 0.000) for 2705 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2700 (Rfree = 0.000) for 2700 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2815 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 9 peptides. Score 0.246 Round 2: 156 peptides, 26 chains. Longest chain 12 peptides. Score 0.422 Round 3: 158 peptides, 25 chains. Longest chain 12 peptides. Score 0.449 Round 4: 166 peptides, 24 chains. Longest chain 17 peptides. Score 0.499 Round 5: 177 peptides, 29 chains. Longest chain 12 peptides. Score 0.455 Taking the results from Round 4 Chains 24, Residues 142, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 5960 restraints for refining 2649 atoms. 5390 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2938 (Rfree = 0.000) for 2649 atoms. Found 11 (20 requested) and removed 20 (10 requested) atoms. Cycle 12: After refmac, R = 0.2764 (Rfree = 0.000) for 2625 atoms. Found 8 (19 requested) and removed 17 (9 requested) atoms. Cycle 13: After refmac, R = 0.2897 (Rfree = 0.000) for 2606 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2742 (Rfree = 0.000) for 2594 atoms. Found 1 (19 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.3136 (Rfree = 0.000) for 2576 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2713 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2728 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 8 peptides. Score 0.300 Round 2: 145 peptides, 28 chains. Longest chain 9 peptides. Score 0.334 Round 3: 153 peptides, 25 chains. Longest chain 12 peptides. Score 0.427 Round 4: 161 peptides, 27 chains. Longest chain 12 peptides. Score 0.425 Round 5: 159 peptides, 25 chains. Longest chain 12 peptides. Score 0.453 Taking the results from Round 5 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 5673 restraints for refining 2564 atoms. 5162 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2843 (Rfree = 0.000) for 2564 atoms. Found 16 (19 requested) and removed 19 (9 requested) atoms. Cycle 17: After refmac, R = 0.2697 (Rfree = 0.000) for 2556 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2693 (Rfree = 0.000) for 2554 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2656 (Rfree = 0.000) for 2549 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2651 (Rfree = 0.000) for 2542 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2652 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2669 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 9 peptides. Score 0.283 Round 2: 161 peptides, 26 chains. Longest chain 11 peptides. Score 0.443 Round 3: 163 peptides, 31 chains. Longest chain 13 peptides. Score 0.358 Round 4: 170 peptides, 29 chains. Longest chain 10 peptides. Score 0.426 Round 5: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 2 Chains 26, Residues 135, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 5833 restraints for refining 2649 atoms. 5280 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2820 (Rfree = 0.000) for 2649 atoms. Found 15 (19 requested) and removed 25 (9 requested) atoms. Cycle 22: After refmac, R = 0.2772 (Rfree = 0.000) for 2637 atoms. Found 2 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2675 (Rfree = 0.000) for 2620 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2743 (Rfree = 0.000) for 2613 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2731 (Rfree = 0.000) for 2606 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 2756 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 2766 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 8 peptides. Score 0.254 Round 2: 159 peptides, 30 chains. Longest chain 13 peptides. Score 0.359 Round 3: 161 peptides, 28 chains. Longest chain 13 peptides. Score 0.406 Round 4: 161 peptides, 28 chains. Longest chain 10 peptides. Score 0.406 Round 5: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.409 Taking the results from Round 5 Chains 29, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6346 restraints for refining 2742 atoms. 5827 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2852 (Rfree = 0.000) for 2742 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 27: After refmac, R = 0.2702 (Rfree = 0.000) for 2741 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.2790 (Rfree = 0.000) for 2728 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2662 (Rfree = 0.000) for 2725 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2702 (Rfree = 0.000) for 2718 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2839 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2845 seeds are put forward Round 1: 130 peptides, 29 chains. Longest chain 7 peptides. Score 0.240 Round 2: 151 peptides, 29 chains. Longest chain 9 peptides. Score 0.342 Round 3: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.409 Round 4: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.385 Round 5: 163 peptides, 28 chains. Longest chain 10 peptides. Score 0.415 Taking the results from Round 5 Chains 28, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6566 restraints for refining 2818 atoms. 6054 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2938 (Rfree = 0.000) for 2818 atoms. Found 6 (21 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.2805 (Rfree = 0.000) for 2799 atoms. Found 4 (21 requested) and removed 14 (10 requested) atoms. Cycle 33: After refmac, R = 0.2815 (Rfree = 0.000) for 2785 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.2711 (Rfree = 0.000) for 2779 atoms. Found 2 (20 requested) and removed 13 (10 requested) atoms. Cycle 35: After refmac, R = 0.2688 (Rfree = 0.000) for 2765 atoms. Found 2 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2878 seeds are put forward NCS extension: 0 residues added, 2878 seeds are put forward Round 1: 120 peptides, 26 chains. Longest chain 8 peptides. Score 0.252 Round 2: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.359 Round 3: 133 peptides, 25 chains. Longest chain 9 peptides. Score 0.337 Round 4: 134 peptides, 25 chains. Longest chain 10 peptides. Score 0.342 Round 5: 135 peptides, 22 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 5 Chains 22, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6538 restraints for refining 2791 atoms. 6108 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2793 (Rfree = 0.000) for 2791 atoms. Found 10 (21 requested) and removed 15 (10 requested) atoms. Cycle 37: After refmac, R = 0.2688 (Rfree = 0.000) for 2782 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2676 (Rfree = 0.000) for 2773 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 39: After refmac, R = 0.2615 (Rfree = 0.000) for 2766 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2574 (Rfree = 0.000) for 2760 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2894 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 9 peptides. Score 0.271 Round 2: 113 peptides, 22 chains. Longest chain 10 peptides. Score 0.302 Round 3: 112 peptides, 21 chains. Longest chain 8 peptides. Score 0.318 Round 4: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.306 Round 5: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.316 Taking the results from Round 3 Chains 21, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6701 restraints for refining 2774 atoms. 6358 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2719 (Rfree = 0.000) for 2774 atoms. Found 18 (20 requested) and removed 31 (10 requested) atoms. Cycle 42: After refmac, R = 0.2663 (Rfree = 0.000) for 2757 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2620 (Rfree = 0.000) for 2749 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2572 (Rfree = 0.000) for 2742 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.2571 (Rfree = 0.000) for 2734 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward NCS extension: 0 residues added, 2835 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 6 peptides. Score 0.225 Round 2: 91 peptides, 19 chains. Longest chain 9 peptides. Score 0.253 Round 3: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.275 Round 4: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.341 Round 5: 103 peptides, 21 chains. Longest chain 10 peptides. Score 0.272 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 89, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5306 reflections ( 99.72 % complete ) and 6673 restraints for refining 2762 atoms. 6336 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2808 (Rfree = 0.000) for 2762 atoms. Found 0 (20 requested) and removed 9 (10 requested) atoms. Cycle 47: After refmac, R = 0.2727 (Rfree = 0.000) for 2752 atoms. Found 0 (20 requested) and removed 2 (10 requested) atoms. Cycle 48: After refmac, R = 0.2709 (Rfree = 0.000) for 2750 atoms. Found 0 (20 requested) and removed 0 (10 requested) atoms. Cycle 49: After refmac, R = 0.2698 (Rfree = 0.000) for 2750 atoms. TimeTaking 28.75