Sun 23 Dec 22:22:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ozg-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-3.4-parrot-hancs ############### 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 22:22:49 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/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-3.4-parrot-hancs/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 290 and 0 Target number of residues in the AU: 290 Target solvent content: 0.6299 Checking the provided sequence file Detected sequence length: 396 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 396 Adjusted target solvent content: 0.49 Input MTZ file: 2ozg-3.4-parrot-hancs.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: 175.031 175.031 71.923 90.000 90.000 120.000 Input sequence file: 2ozg-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3168 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.516 3.400 Wilson plot Bfac: 66.14 5896 reflections ( 99.76 % complete ) and 0 restraints for refining 3520 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3180 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3309 (Rfree = 0.000) for 3520 atoms. Found 26 (26 requested) and removed 53 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 3581 seeds are put forward Round 1: 172 peptides, 37 chains. Longest chain 8 peptides. Score 0.271 Round 2: 208 peptides, 37 chains. Longest chain 15 peptides. Score 0.412 Round 3: 225 peptides, 35 chains. Longest chain 14 peptides. Score 0.501 Round 4: 224 peptides, 34 chains. Longest chain 14 peptides. Score 0.512 Round 5: 211 peptides, 32 chains. Longest chain 13 peptides. Score 0.498 Taking the results from Round 4 Chains 34, Residues 190, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 6384 restraints for refining 2879 atoms. 5643 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2559 (Rfree = 0.000) for 2879 atoms. Found 10 (21 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.2705 (Rfree = 0.000) for 2838 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 3: After refmac, R = 0.2516 (Rfree = 0.000) for 2810 atoms. Found 14 (21 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.2551 (Rfree = 0.000) for 2787 atoms. Found 13 (21 requested) and removed 24 (10 requested) atoms. Cycle 5: After refmac, R = 0.2705 (Rfree = 0.000) for 2760 atoms. Found 16 (20 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 2901 seeds are put forward Round 1: 172 peptides, 32 chains. Longest chain 11 peptides. Score 0.356 Round 2: 212 peptides, 32 chains. Longest chain 14 peptides. Score 0.501 Round 3: 206 peptides, 33 chains. Longest chain 16 peptides. Score 0.466 Round 4: 219 peptides, 30 chains. Longest chain 15 peptides. Score 0.551 Round 5: 214 peptides, 29 chains. Longest chain 16 peptides. Score 0.550 Taking the results from Round 4 Chains 30, Residues 189, Estimated correctness of the model 11.9 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 6371 restraints for refining 2880 atoms. 5609 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2414 (Rfree = 0.000) for 2880 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 7: After refmac, R = 0.2386 (Rfree = 0.000) for 2855 atoms. Found 19 (21 requested) and removed 16 (10 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 2841 atoms. Found 9 (21 requested) and removed 14 (10 requested) atoms. Cycle 9: After refmac, R = 0.1952 (Rfree = 0.000) for 2822 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2286 (Rfree = 0.000) for 2813 atoms. Found 19 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward Round 1: 181 peptides, 33 chains. Longest chain 12 peptides. Score 0.374 Round 2: 203 peptides, 33 chains. Longest chain 15 peptides. Score 0.455 Round 3: 219 peptides, 35 chains. Longest chain 13 peptides. Score 0.481 Round 4: 213 peptides, 28 chains. Longest chain 20 peptides. Score 0.560 Round 5: 223 peptides, 31 chains. Longest chain 20 peptides. Score 0.550 Taking the results from Round 4 Chains 28, Residues 185, Estimated correctness of the model 15.1 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 6288 restraints for refining 2878 atoms. 5513 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2418 (Rfree = 0.000) for 2878 atoms. Found 20 (21 requested) and removed 16 (10 requested) atoms. Cycle 12: After refmac, R = 0.2771 (Rfree = 0.000) for 2856 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 13: After refmac, R = 0.2136 (Rfree = 0.000) for 2829 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. Cycle 14: After refmac, R = 0.2079 (Rfree = 0.000) for 2821 atoms. Found 17 (21 requested) and removed 17 (10 requested) atoms. Cycle 15: After refmac, R = 0.1747 (Rfree = 0.000) for 2814 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward Round 1: 184 peptides, 34 chains. Longest chain 15 peptides. Score 0.369 Round 2: 212 peptides, 32 chains. Longest chain 26 peptides. Score 0.501 Round 3: 202 peptides, 32 chains. Longest chain 22 peptides. Score 0.467 Round 4: 217 peptides, 30 chains. Longest chain 22 peptides. Score 0.545 Round 5: 212 peptides, 30 chains. Longest chain 30 peptides. Score 0.530 Taking the results from Round 4 Chains 33, Residues 187, Estimated correctness of the model 9.7 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 5877 restraints for refining 2880 atoms. 4996 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2141 (Rfree = 0.000) for 2880 atoms. Found 20 (21 requested) and removed 18 (10 requested) atoms. Cycle 17: After refmac, R = 0.2003 (Rfree = 0.000) for 2858 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. Cycle 18: After refmac, R = 0.2002 (Rfree = 0.000) for 2848 atoms. Found 12 (21 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.1960 (Rfree = 0.000) for 2844 atoms. Found 20 (21 requested) and removed 16 (10 requested) atoms. Cycle 20: After refmac, R = 0.1980 (Rfree = 0.000) for 2841 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2962 seeds are put forward Round 1: 155 peptides, 27 chains. Longest chain 16 peptides. Score 0.373 Round 2: 184 peptides, 30 chains. Longest chain 17 peptides. Score 0.434 Round 3: 205 peptides, 30 chains. Longest chain 20 peptides. Score 0.507 Round 4: 209 peptides, 30 chains. Longest chain 23 peptides. Score 0.520 Round 5: 192 peptides, 28 chains. Longest chain 14 peptides. Score 0.493 Taking the results from Round 4 Chains 30, Residues 179, Estimated correctness of the model 0.4 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5896 reflections ( 99.76 % complete ) and 6453 restraints for refining 2876 atoms. 5756 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2149 (Rfree = 0.000) for 2876 atoms. Found 16 (21 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.1936 (Rfree = 0.000) for 2865 atoms. Found 10 (21 requested) and removed 15 (10 requested) atoms. Cycle 23: After refmac, R = 0.1944 (Rfree = 0.000) for 2853 atoms. Found 12 (21 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.2296 (Rfree = 0.000) for 2841 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.1734 (Rfree = 0.000) for 2831 atoms. Found 11 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward Round 1: 178 peptides, 33 chains. Longest chain 19 peptides. Score 0.363 Round 2: 214 peptides, 31 chains. Longest chain 26 peptides. Score 0.522 Round 3: 200 peptides, 29 chains. Longest chain 26 peptides. Score 0.505 Round 4: 210 peptides, 32 chains. Longest chain 16 peptides. Score 0.494 Round 5: 213 peptides, 30 chains. Longest chain 22 peptides. Score 0.533 Taking the results from Round 5 Chains 31, Residues 183, Estimated correctness of the model 5.3 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 6247 restraints for refining 2880 atoms. 5488 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2159 (Rfree = 0.000) for 2880 atoms. Found 19 (21 requested) and removed 17 (10 requested) atoms. Cycle 27: After refmac, R = 0.2553 (Rfree = 0.000) for 2864 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 28: After refmac, R = 0.1919 (Rfree = 0.000) for 2854 atoms. Found 9 (21 requested) and removed 18 (10 requested) atoms. Cycle 29: After refmac, R = 0.2206 (Rfree = 0.000) for 2842 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 30: After refmac, R = 0.1898 (Rfree = 0.000) for 2847 atoms. Found 11 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward Round 1: 180 peptides, 30 chains. Longest chain 21 peptides. Score 0.419 Round 2: 201 peptides, 30 chains. Longest chain 28 peptides. Score 0.494 Round 3: 201 peptides, 29 chains. Longest chain 22 peptides. Score 0.508 Round 4: 209 peptides, 30 chains. Longest chain 17 peptides. Score 0.520 Round 5: 213 peptides, 31 chains. Longest chain 21 peptides. Score 0.519 Taking the results from Round 4 Chains 31, Residues 179, Estimated correctness of the model 0.4 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 6164 restraints for refining 2880 atoms. 5406 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2284 (Rfree = 0.000) for 2880 atoms. Found 18 (21 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.1910 (Rfree = 0.000) for 2875 atoms. Found 10 (21 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2214 (Rfree = 0.000) for 2867 atoms. Found 19 (21 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.1922 (Rfree = 0.000) for 2870 atoms. Found 17 (21 requested) and removed 14 (10 requested) atoms. Cycle 35: After refmac, R = 0.2141 (Rfree = 0.000) for 2869 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward Round 1: 158 peptides, 29 chains. Longest chain 12 peptides. Score 0.351 Round 2: 165 peptides, 25 chains. Longest chain 18 peptides. Score 0.445 Round 3: 180 peptides, 28 chains. Longest chain 14 peptides. Score 0.451 Round 4: 187 peptides, 25 chains. Longest chain 25 peptides. Score 0.521 Round 5: 185 peptides, 22 chains. Longest chain 25 peptides. Score 0.558 Taking the results from Round 5 Chains 25, Residues 163, Estimated correctness of the model 14.4 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5896 reflections ( 99.76 % complete ) and 6077 restraints for refining 2880 atoms. 5337 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2094 (Rfree = 0.000) for 2880 atoms. Found 12 (21 requested) and removed 16 (10 requested) atoms. Cycle 37: After refmac, R = 0.2118 (Rfree = 0.000) for 2872 atoms. Found 19 (21 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 2874 atoms. Found 15 (21 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.1688 (Rfree = 0.000) for 2870 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1620 (Rfree = 0.000) for 2866 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 10 peptides. Score 0.285 Round 2: 182 peptides, 30 chains. Longest chain 12 peptides. Score 0.427 Round 3: 172 peptides, 30 chains. Longest chain 10 peptides. Score 0.389 Round 4: 169 peptides, 29 chains. Longest chain 14 peptides. Score 0.394 Round 5: 190 peptides, 28 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 5 Chains 28, Residues 162, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5896 reflections ( 99.76 % complete ) and 6368 restraints for refining 2880 atoms. 5697 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2134 (Rfree = 0.000) for 2880 atoms. Found 19 (21 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2119 (Rfree = 0.000) for 2882 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.1832 (Rfree = 0.000) for 2890 atoms. Found 10 (21 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.1729 (Rfree = 0.000) for 2885 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1726 (Rfree = 0.000) for 2875 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 10 peptides. Score 0.294 Round 2: 190 peptides, 34 chains. Longest chain 10 peptides. Score 0.392 Round 3: 189 peptides, 32 chains. Longest chain 14 peptides. Score 0.421 Round 4: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.394 Round 5: 185 peptides, 29 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 156, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2ozg-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (156 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5896 reflections ( 99.76 % complete ) and 6494 restraints for refining 2880 atoms. 5878 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2217 (Rfree = 0.000) for 2880 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2470 (Rfree = 0.000) for 2864 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2020 (Rfree = 0.000) for 2846 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1750 (Rfree = 0.000) for 2834 atoms. TimeTaking 58.15