Mon 24 Dec 07:39:25 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 2ogi-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-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/2ogi-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-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 07:39:30 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/2ogi-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-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 281 and 0 Target number of residues in the AU: 281 Target solvent content: 0.6557 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: 0.52 Input MTZ file: 2ogi-3.6-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.90 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: 63.833 3.600 Wilson plot Bfac: 81.58 5214 reflections ( 99.79 % complete ) and 0 restraints for refining 3453 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3574 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3241 (Rfree = 0.000) for 3453 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 3533 seeds are put forward NCS extension: 0 residues added, 3533 seeds are put forward Round 1: 147 peptides, 28 chains. Longest chain 12 peptides. Score 0.319 Round 2: 196 peptides, 32 chains. Longest chain 13 peptides. Score 0.437 Round 3: 198 peptides, 33 chains. Longest chain 15 peptides. Score 0.429 Round 4: 211 peptides, 33 chains. Longest chain 15 peptides. Score 0.473 Round 5: 214 peptides, 33 chains. Longest chain 15 peptides. Score 0.483 Taking the results from Round 5 Chains 33, Residues 181, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6404 restraints for refining 2843 atoms. 5633 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2574 (Rfree = 0.000) for 2843 atoms. Found 10 (18 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2447 (Rfree = 0.000) for 2770 atoms. Found 10 (18 requested) and removed 21 (9 requested) atoms. Cycle 3: After refmac, R = 0.2158 (Rfree = 0.000) for 2731 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2237 (Rfree = 0.000) for 2715 atoms. Found 8 (17 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2157 (Rfree = 0.000) for 2701 atoms. Found 12 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 2852 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2866 seeds are put forward Round 1: 173 peptides, 34 chains. Longest chain 10 peptides. Score 0.321 Round 2: 208 peptides, 34 chains. Longest chain 15 peptides. Score 0.449 Round 3: 217 peptides, 32 chains. Longest chain 31 peptides. Score 0.507 Round 4: 206 peptides, 32 chains. Longest chain 16 peptides. Score 0.471 Round 5: 207 peptides, 30 chains. Longest chain 17 peptides. Score 0.503 Taking the results from Round 3 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 5944 restraints for refining 2759 atoms. 5176 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2675 (Rfree = 0.000) for 2759 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 7: After refmac, R = 0.2571 (Rfree = 0.000) for 2715 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 8: After refmac, R = 0.2485 (Rfree = 0.000) for 2682 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.2353 (Rfree = 0.000) for 2672 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.2505 (Rfree = 0.000) for 2665 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 2765 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2779 seeds are put forward Round 1: 159 peptides, 32 chains. Longest chain 10 peptides. Score 0.299 Round 2: 175 peptides, 28 chains. Longest chain 10 peptides. Score 0.425 Round 3: 181 peptides, 29 chains. Longest chain 13 peptides. Score 0.431 Round 4: 193 peptides, 29 chains. Longest chain 23 peptides. Score 0.472 Round 5: 193 peptides, 29 chains. Longest chain 17 peptides. Score 0.472 Taking the results from Round 5 Chains 29, Residues 164, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6383 restraints for refining 2830 atoms. 5713 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2903 (Rfree = 0.000) for 2830 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 12: After refmac, R = 0.2651 (Rfree = 0.000) for 2778 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 13: After refmac, R = 0.2689 (Rfree = 0.000) for 2753 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 14: After refmac, R = 0.2709 (Rfree = 0.000) for 2729 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 15: After refmac, R = 0.2492 (Rfree = 0.000) for 2713 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 2853 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2875 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 11 peptides. Score 0.322 Round 2: 170 peptides, 31 chains. Longest chain 11 peptides. Score 0.359 Round 3: 192 peptides, 32 chains. Longest chain 16 peptides. Score 0.423 Round 4: 199 peptides, 30 chains. Longest chain 24 peptides. Score 0.477 Round 5: 192 peptides, 30 chains. Longest chain 17 peptides. Score 0.454 Taking the results from Round 4 Chains 33, Residues 169, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6078 restraints for refining 2811 atoms. 5373 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2778 (Rfree = 0.000) for 2811 atoms. Found 18 (18 requested) and removed 66 (9 requested) atoms. Cycle 17: After refmac, R = 0.2642 (Rfree = 0.000) for 2729 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 2699 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 19: After refmac, R = 0.2547 (Rfree = 0.000) for 2687 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2532 (Rfree = 0.000) for 2683 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.54 Search for helices and strands: 0 residues in 0 chains, 2796 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2813 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 9 peptides. Score 0.252 Round 2: 159 peptides, 28 chains. Longest chain 10 peptides. Score 0.366 Round 3: 161 peptides, 28 chains. Longest chain 17 peptides. Score 0.373 Round 4: 168 peptides, 28 chains. Longest chain 11 peptides. Score 0.400 Round 5: 160 peptides, 26 chains. Longest chain 14 peptides. Score 0.402 Taking the results from Round 5 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6490 restraints for refining 2843 atoms. 5951 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2593 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 22: After refmac, R = 0.2371 (Rfree = 0.000) for 2795 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 23: After refmac, R = 0.2368 (Rfree = 0.000) for 2787 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 24: After refmac, R = 0.2250 (Rfree = 0.000) for 2777 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1885 (Rfree = 0.000) for 2769 atoms. Found 7 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 2868 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2886 seeds are put forward Round 1: 135 peptides, 29 chains. Longest chain 8 peptides. Score 0.252 Round 2: 153 peptides, 30 chains. Longest chain 9 peptides. Score 0.309 Round 3: 156 peptides, 27 chains. Longest chain 10 peptides. Score 0.371 Round 4: 158 peptides, 30 chains. Longest chain 9 peptides. Score 0.329 Round 5: 163 peptides, 29 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 3 Chains 27, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6749 restraints for refining 2843 atoms. 6260 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2540 (Rfree = 0.000) for 2843 atoms. Found 16 (18 requested) and removed 24 (9 requested) atoms. Cycle 27: After refmac, R = 0.2344 (Rfree = 0.000) for 2824 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 28: After refmac, R = 0.2330 (Rfree = 0.000) for 2811 atoms. Found 10 (18 requested) and removed 18 (9 requested) atoms. Cycle 29: After refmac, R = 0.2268 (Rfree = 0.000) for 2799 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 30: After refmac, R = 0.2199 (Rfree = 0.000) for 2794 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 2912 seeds are put forward NCS extension: 0 residues added, 2912 seeds are put forward Round 1: 118 peptides, 27 chains. Longest chain 7 peptides. Score 0.213 Round 2: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.258 Round 3: 121 peptides, 24 chains. Longest chain 9 peptides. Score 0.282 Round 4: 134 peptides, 27 chains. Longest chain 9 peptides. Score 0.283 Round 5: 139 peptides, 25 chains. Longest chain 10 peptides. Score 0.338 Taking the results from Round 5 Chains 25, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6624 restraints for refining 2843 atoms. 6193 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2078 (Rfree = 0.000) for 2843 atoms. Found 11 (18 requested) and removed 20 (9 requested) atoms. Cycle 32: After refmac, R = 0.2079 (Rfree = 0.000) for 2813 atoms. Found 16 (18 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.2070 (Rfree = 0.000) for 2805 atoms. Found 9 (18 requested) and removed 17 (9 requested) atoms. Cycle 34: After refmac, R = 0.1931 (Rfree = 0.000) for 2793 atoms. Found 10 (17 requested) and removed 16 (8 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1853 (Rfree = 0.000) for 2785 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 2900 seeds are put forward NCS extension: 0 residues added, 2900 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 8 peptides. Score 0.251 Round 2: 123 peptides, 25 chains. Longest chain 12 peptides. Score 0.272 Round 3: 120 peptides, 23 chains. Longest chain 8 peptides. Score 0.296 Round 4: 120 peptides, 23 chains. Longest chain 8 peptides. Score 0.296 Round 5: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 5 Chains 20, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6516 restraints for refining 2843 atoms. 6136 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2212 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 37: After refmac, R = 0.2004 (Rfree = 0.000) for 2834 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.1899 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.1855 (Rfree = 0.000) for 2827 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1817 (Rfree = 0.000) for 2830 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 2909 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2915 seeds are put forward Round 1: 90 peptides, 21 chains. Longest chain 6 peptides. Score 0.197 Round 2: 119 peptides, 26 chains. Longest chain 11 peptides. Score 0.236 Round 3: 121 peptides, 24 chains. Longest chain 10 peptides. Score 0.282 Round 4: 129 peptides, 24 chains. Longest chain 10 peptides. Score 0.315 Round 5: 127 peptides, 21 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 5 Chains 21, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6536 restraints for refining 2843 atoms. 6133 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2167 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 42: After refmac, R = 0.2023 (Rfree = 0.000) for 2835 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2049 (Rfree = 0.000) for 2835 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1883 (Rfree = 0.000) for 2826 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 45: After refmac, R = 0.1972 (Rfree = 0.000) for 2825 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 2918 seeds are put forward NCS extension: 0 residues added, 2918 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.214 Round 2: 100 peptides, 21 chains. Longest chain 7 peptides. Score 0.245 Round 3: 107 peptides, 22 chains. Longest chain 7 peptides. Score 0.258 Round 4: 118 peptides, 22 chains. Longest chain 12 peptides. Score 0.306 Round 5: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 96, 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 2ogi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5214 reflections ( 99.79 % complete ) and 6463 restraints for refining 2775 atoms. 6101 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2113 (Rfree = 0.000) for 2775 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2155 (Rfree = 0.000) for 2758 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1976 (Rfree = 0.000) for 2746 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1604 (Rfree = 0.000) for 2732 atoms. TimeTaking 35.5