Mon 24 Dec 07:26:49 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 2oyo-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-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/2oyo-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-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 07:26:54 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/2oyo-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.6714 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.80 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: 83.295 4.001 Wilson plot Bfac: 93.40 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3640 reflections ( 99.75 % complete ) and 0 restraints for refining 3497 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3418 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3046 (Rfree = 0.000) for 3497 atoms. Found 16 (16 requested) and removed 40 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 3.90 Search for helices and strands: 0 residues in 0 chains, 3554 seeds are put forward NCS extension: 0 residues added, 3554 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 9 peptides. Score 0.271 Round 2: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.410 Round 3: 165 peptides, 27 chains. Longest chain 13 peptides. Score 0.414 Round 4: 173 peptides, 25 chains. Longest chain 17 peptides. Score 0.476 Round 5: 185 peptides, 25 chains. Longest chain 21 peptides. Score 0.517 Taking the results from Round 5 Chains 26, Residues 160, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6597 restraints for refining 2827 atoms. 5916 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2399 (Rfree = 0.000) for 2827 atoms. Found 8 (13 requested) and removed 28 (6 requested) atoms. Cycle 2: After refmac, R = 0.2244 (Rfree = 0.000) for 2776 atoms. Found 5 (13 requested) and removed 21 (6 requested) atoms. Cycle 3: After refmac, R = 0.2096 (Rfree = 0.000) for 2741 atoms. Found 8 (13 requested) and removed 17 (6 requested) atoms. Cycle 4: After refmac, R = 0.1638 (Rfree = 0.000) for 2714 atoms. Found 3 (12 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.1501 (Rfree = 0.000) for 2696 atoms. Found 0 (12 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 2813 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 2838 seeds are put forward Round 1: 159 peptides, 31 chains. Longest chain 13 peptides. Score 0.322 Round 2: 159 peptides, 25 chains. Longest chain 15 peptides. Score 0.425 Round 3: 178 peptides, 28 chains. Longest chain 14 peptides. Score 0.446 Round 4: 175 peptides, 28 chains. Longest chain 11 peptides. Score 0.435 Round 5: 172 peptides, 26 chains. Longest chain 14 peptides. Score 0.457 Taking the results from Round 5 Chains 26, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6834 restraints for refining 2832 atoms. 6276 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2180 (Rfree = 0.000) for 2832 atoms. Found 12 (13 requested) and removed 31 (6 requested) atoms. Cycle 7: After refmac, R = 0.2121 (Rfree = 0.000) for 2793 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 8: After refmac, R = 0.2024 (Rfree = 0.000) for 2759 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 9: After refmac, R = 0.1998 (Rfree = 0.000) for 2739 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 10: After refmac, R = 0.1862 (Rfree = 0.000) for 2721 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 2870 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2884 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 8 peptides. Score 0.264 Round 2: 161 peptides, 30 chains. Longest chain 13 peptides. Score 0.348 Round 3: 173 peptides, 28 chains. Longest chain 11 peptides. Score 0.428 Round 4: 172 peptides, 29 chains. Longest chain 12 peptides. Score 0.408 Round 5: 174 peptides, 27 chains. Longest chain 10 peptides. Score 0.448 Taking the results from Round 5 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6677 restraints for refining 2832 atoms. 6089 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2045 (Rfree = 0.000) for 2832 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 12: After refmac, R = 0.2161 (Rfree = 0.000) for 2801 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 2767 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1965 (Rfree = 0.000) for 2744 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 15: After refmac, R = 0.2116 (Rfree = 0.000) for 2724 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 2863 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2875 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 9 peptides. Score 0.265 Round 2: 159 peptides, 29 chains. Longest chain 11 peptides. Score 0.357 Round 3: 158 peptides, 28 chains. Longest chain 17 peptides. Score 0.370 Round 4: 168 peptides, 27 chains. Longest chain 15 peptides. Score 0.426 Round 5: 169 peptides, 29 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 4 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6676 restraints for refining 2802 atoms. 6139 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2045 (Rfree = 0.000) for 2802 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 17: After refmac, R = 0.2177 (Rfree = 0.000) for 2782 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 18: After refmac, R = 0.2190 (Rfree = 0.000) for 2762 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 19: After refmac, R = 0.2153 (Rfree = 0.000) for 2735 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.2051 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 2860 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2872 seeds are put forward Round 1: 112 peptides, 23 chains. Longest chain 8 peptides. Score 0.265 Round 2: 142 peptides, 28 chains. Longest chain 10 peptides. Score 0.304 Round 3: 144 peptides, 28 chains. Longest chain 9 peptides. Score 0.312 Round 4: 151 peptides, 24 chains. Longest chain 12 peptides. Score 0.411 Round 5: 142 peptides, 27 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 4 Chains 24, Residues 127, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6132 restraints for refining 2758 atoms. 5555 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2062 (Rfree = 0.000) for 2758 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 22: After refmac, R = 0.2198 (Rfree = 0.000) for 2717 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.1985 (Rfree = 0.000) for 2703 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 24: After refmac, R = 0.1543 (Rfree = 0.000) for 2687 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1453 (Rfree = 0.000) for 2677 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 2778 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2795 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 6 peptides. Score 0.216 Round 2: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.340 Round 3: 143 peptides, 27 chains. Longest chain 9 peptides. Score 0.326 Round 4: 142 peptides, 24 chains. Longest chain 11 peptides. Score 0.375 Round 5: 143 peptides, 26 chains. Longest chain 12 peptides. Score 0.344 Taking the results from Round 4 Chains 24, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6179 restraints for refining 2662 atoms. 5731 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1928 (Rfree = 0.000) for 2662 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.2294 (Rfree = 0.000) for 2648 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 28: After refmac, R = 0.2015 (Rfree = 0.000) for 2617 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 29: After refmac, R = 0.2083 (Rfree = 0.000) for 2603 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.1869 (Rfree = 0.000) for 2596 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 2734 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2748 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 8 peptides. Score 0.227 Round 2: 137 peptides, 27 chains. Longest chain 8 peptides. Score 0.301 Round 3: 137 peptides, 24 chains. Longest chain 10 peptides. Score 0.355 Round 4: 138 peptides, 24 chains. Longest chain 12 peptides. Score 0.359 Round 5: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Chains 23, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6285 restraints for refining 2668 atoms. 5856 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2069 (Rfree = 0.000) for 2668 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 32: After refmac, R = 0.2004 (Rfree = 0.000) for 2637 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.1949 (Rfree = 0.000) for 2615 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.1415 (Rfree = 0.000) for 2607 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1308 (Rfree = 0.000) for 2593 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 2703 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2715 seeds are put forward Round 1: 101 peptides, 24 chains. Longest chain 5 peptides. Score 0.192 Round 2: 124 peptides, 26 chains. Longest chain 7 peptides. Score 0.262 Round 3: 133 peptides, 26 chains. Longest chain 11 peptides. Score 0.302 Round 4: 143 peptides, 26 chains. Longest chain 13 peptides. Score 0.344 Round 5: 148 peptides, 26 chains. Longest chain 18 peptides. Score 0.364 Taking the results from Round 5 Chains 26, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6152 restraints for refining 2628 atoms. 5690 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1925 (Rfree = 0.000) for 2628 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 37: After refmac, R = 0.1875 (Rfree = 0.000) for 2601 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 38: After refmac, R = 0.1911 (Rfree = 0.000) for 2588 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 39: After refmac, R = 0.1841 (Rfree = 0.000) for 2579 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.1827 (Rfree = 0.000) for 2577 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 2686 seeds are put forward NCS extension: 0 residues added, 2686 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 7 peptides. Score 0.227 Round 2: 120 peptides, 21 chains. Longest chain 15 peptides. Score 0.339 Round 3: 129 peptides, 25 chains. Longest chain 9 peptides. Score 0.303 Round 4: 125 peptides, 24 chains. Longest chain 13 peptides. Score 0.304 Round 5: 116 peptides, 21 chains. Longest chain 13 peptides. Score 0.321 Taking the results from Round 2 Chains 21, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 5948 restraints for refining 2575 atoms. 5573 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1950 (Rfree = 0.000) for 2575 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.1719 (Rfree = 0.000) for 2566 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 2558 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.1859 (Rfree = 0.000) for 2557 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.1782 (Rfree = 0.000) for 2547 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.78 Search for helices and strands: 0 residues in 0 chains, 2669 seeds are put forward NCS extension: 0 residues added, 2669 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 9 peptides. Score 0.233 Round 2: 88 peptides, 18 chains. Longest chain 14 peptides. Score 0.252 Round 3: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.268 Round 4: 96 peptides, 16 chains. Longest chain 14 peptides. Score 0.331 Round 5: 96 peptides, 16 chains. Longest chain 15 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 80, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2oyo-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3640 reflections ( 99.75 % complete ) and 6104 restraints for refining 2617 atoms. 5779 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2013 (Rfree = 0.000) for 2617 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2046 (Rfree = 0.000) for 2605 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1762 (Rfree = 0.000) for 2594 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1564 (Rfree = 0.000) for 2586 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 37.15