null Mon 24 Dec 07:40:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i51-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i51-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i51-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-parrot-noncs ############### 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 07:40:20 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/noncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-parrot-noncs/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 314 and 0 Target number of residues in the AU: 314 Target solvent content: 0.6504 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-4.0-parrot-noncs.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: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3120 target number of atoms Had to go as low as 0.85 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: 56.880 4.000 Wilson plot Bfac: 77.89 3751 reflections ( 84.54 % complete ) and 0 restraints for refining 3455 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3571 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3524 (Rfree = 0.000) for 3455 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 3477 seeds are put forward NCS extension: 0 residues added, 3477 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 7 peptides. Score 0.223 Round 2: 154 peptides, 31 chains. Longest chain 8 peptides. Score 0.287 Round 3: 158 peptides, 28 chains. Longest chain 13 peptides. Score 0.349 Round 4: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.385 Round 5: 173 peptides, 29 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 5 Chains 29, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6585 restraints for refining 2813 atoms. 6038 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3065 (Rfree = 0.000) for 2813 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 2: After refmac, R = 0.3024 (Rfree = 0.000) for 2756 atoms. Found 7 (13 requested) and removed 18 (6 requested) atoms. Cycle 3: After refmac, R = 0.2812 (Rfree = 0.000) for 2708 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2858 (Rfree = 0.000) for 2676 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 5: After refmac, R = 0.2574 (Rfree = 0.000) for 2663 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 2710 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2717 seeds are put forward Round 1: 130 peptides, 28 chains. Longest chain 8 peptides. Score 0.243 Round 2: 171 peptides, 32 chains. Longest chain 10 peptides. Score 0.334 Round 3: 176 peptides, 29 chains. Longest chain 14 peptides. Score 0.396 Round 4: 173 peptides, 29 chains. Longest chain 15 peptides. Score 0.386 Round 5: 187 peptides, 30 chains. Longest chain 16 peptides. Score 0.418 Taking the results from Round 5 Chains 30, Residues 157, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 5773 restraints for refining 2601 atoms. 5141 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2609 (Rfree = 0.000) for 2601 atoms. Found 11 (12 requested) and removed 17 (6 requested) atoms. Cycle 7: After refmac, R = 0.2427 (Rfree = 0.000) for 2564 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 8: After refmac, R = 0.2475 (Rfree = 0.000) for 2532 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2540 (Rfree = 0.000) for 2524 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2275 (Rfree = 0.000) for 2507 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 2550 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2580 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 7 peptides. Score 0.262 Round 2: 184 peptides, 35 chains. Longest chain 11 peptides. Score 0.335 Round 3: 183 peptides, 31 chains. Longest chain 12 peptides. Score 0.391 Round 4: 184 peptides, 31 chains. Longest chain 12 peptides. Score 0.394 Round 5: 188 peptides, 30 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 5 Chains 31, Residues 158, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 5850 restraints for refining 2691 atoms. 5206 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2663 (Rfree = 0.000) for 2691 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 12: After refmac, R = 0.2283 (Rfree = 0.000) for 2660 atoms. Found 11 (12 requested) and removed 26 (6 requested) atoms. Cycle 13: After refmac, R = 0.2361 (Rfree = 0.000) for 2631 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.2132 (Rfree = 0.000) for 2618 atoms. Found 5 (12 requested) and removed 22 (6 requested) atoms. Cycle 15: After refmac, R = 0.2324 (Rfree = 0.000) for 2594 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 2631 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2648 seeds are put forward Round 1: 156 peptides, 30 chains. Longest chain 11 peptides. Score 0.310 Round 2: 169 peptides, 30 chains. Longest chain 10 peptides. Score 0.357 Round 3: 185 peptides, 27 chains. Longest chain 13 peptides. Score 0.455 Round 4: 169 peptides, 24 chains. Longest chain 14 peptides. Score 0.447 Round 5: 176 peptides, 24 chains. Longest chain 16 peptides. Score 0.469 Taking the results from Round 5 Chains 24, Residues 152, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6010 restraints for refining 2817 atoms. 5288 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2447 (Rfree = 0.000) for 2817 atoms. Found 12 (13 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.2544 (Rfree = 0.000) for 2772 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 18: After refmac, R = 0.2452 (Rfree = 0.000) for 2746 atoms. Found 10 (13 requested) and removed 15 (6 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 2718 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2269 (Rfree = 0.000) for 2696 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 2742 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2765 seeds are put forward Round 1: 124 peptides, 28 chains. Longest chain 6 peptides. Score 0.218 Round 2: 167 peptides, 30 chains. Longest chain 11 peptides. Score 0.350 Round 3: 168 peptides, 31 chains. Longest chain 11 peptides. Score 0.339 Round 4: 164 peptides, 28 chains. Longest chain 10 peptides. Score 0.370 Round 5: 165 peptides, 30 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 4 Chains 28, Residues 136, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6492 restraints for refining 2817 atoms. 5947 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2363 (Rfree = 0.000) for 2817 atoms. Found 11 (13 requested) and removed 19 (6 requested) atoms. Cycle 22: After refmac, R = 0.1929 (Rfree = 0.000) for 2791 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.2021 (Rfree = 0.000) for 2774 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.1714 (Rfree = 0.000) for 2769 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 25: After refmac, R = 0.2041 (Rfree = 0.000) for 2753 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.28 Search for helices and strands: 0 residues in 0 chains, 2812 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2821 seeds are put forward Round 1: 150 peptides, 33 chains. Longest chain 9 peptides. Score 0.240 Round 2: 162 peptides, 30 chains. Longest chain 10 peptides. Score 0.332 Round 3: 168 peptides, 31 chains. Longest chain 15 peptides. Score 0.339 Round 4: 183 peptides, 31 chains. Longest chain 11 peptides. Score 0.391 Round 5: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 4 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6545 restraints for refining 2817 atoms. 5968 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2304 (Rfree = 0.000) for 2817 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.2408 (Rfree = 0.000) for 2790 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 28: After refmac, R = 0.2197 (Rfree = 0.000) for 2772 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.1802 (Rfree = 0.000) for 2761 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1681 (Rfree = 0.000) for 2751 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2783 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2796 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 10 peptides. Score 0.262 Round 2: 152 peptides, 30 chains. Longest chain 10 peptides. Score 0.296 Round 3: 160 peptides, 31 chains. Longest chain 9 peptides. Score 0.310 Round 4: 161 peptides, 29 chains. Longest chain 11 peptides. Score 0.344 Round 5: 162 peptides, 29 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 5 Chains 29, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6627 restraints for refining 2817 atoms. 6124 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2229 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. Cycle 32: After refmac, R = 0.2029 (Rfree = 0.000) for 2782 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 33: After refmac, R = 0.2350 (Rfree = 0.000) for 2772 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.1586 (Rfree = 0.000) for 2761 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1616 (Rfree = 0.000) for 2751 atoms. Found 8 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2788 seeds are put forward NCS extension: 0 residues added, 2788 seeds are put forward Round 1: 126 peptides, 29 chains. Longest chain 6 peptides. Score 0.209 Round 2: 131 peptides, 27 chains. Longest chain 8 peptides. Score 0.264 Round 3: 125 peptides, 24 chains. Longest chain 9 peptides. Score 0.290 Round 4: 133 peptides, 26 chains. Longest chain 8 peptides. Score 0.288 Round 5: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 5 Chains 28, Residues 124, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6440 restraints for refining 2816 atoms. 5952 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2414 (Rfree = 0.000) for 2816 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.2523 (Rfree = 0.000) for 2790 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2113 (Rfree = 0.000) for 2778 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 39: After refmac, R = 0.2031 (Rfree = 0.000) for 2762 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.1987 (Rfree = 0.000) for 2758 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 2803 seeds are put forward NCS extension: 0 residues added, 2803 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 8 peptides. Score 0.221 Round 2: 129 peptides, 21 chains. Longest chain 15 peptides. Score 0.356 Round 3: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.284 Round 4: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.296 Round 5: 118 peptides, 21 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 2 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6360 restraints for refining 2752 atoms. 5949 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2330 (Rfree = 0.000) for 2752 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 42: After refmac, R = 0.2419 (Rfree = 0.000) for 2734 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.2187 (Rfree = 0.000) for 2722 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 44: After refmac, R = 0.2476 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 45: After refmac, R = 0.2229 (Rfree = 0.000) for 2705 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2748 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2767 seeds are put forward Round 1: 88 peptides, 21 chains. Longest chain 5 peptides. Score 0.186 Round 2: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.250 Round 3: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.229 Round 4: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.269 Round 5: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.265 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 79, 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 2i51-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3751 reflections ( 84.54 % complete ) and 6225 restraints for refining 2664 atoms. 5928 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2628 (Rfree = 0.000) for 2664 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2420 (Rfree = 0.000) for 2647 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1850 (Rfree = 0.000) for 2637 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2206 (Rfree = 0.000) for 2629 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:13:56 GMT 2018 Job finished. TimeTaking 33.68 Used memory is bytes: 7136104