Sun 23 Dec 22:22:44 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 2oyo-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-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/2oyo-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-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 22:22:53 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/2oyo-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-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 279 and 0 Target number of residues in the AU: 279 Target solvent content: 0.6391 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-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: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 70.81 5885 reflections ( 99.85 % complete ) and 0 restraints for refining 3522 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3128 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2874 (Rfree = 0.000) for 3522 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 0 residues added, 3627 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 9 peptides. Score 0.293 Round 2: 208 peptides, 35 chains. Longest chain 15 peptides. Score 0.445 Round 3: 238 peptides, 36 chains. Longest chain 12 peptides. Score 0.532 Round 4: 245 peptides, 30 chains. Longest chain 30 peptides. Score 0.630 Round 5: 245 peptides, 33 chains. Longest chain 17 peptides. Score 0.592 Taking the results from Round 4 Chains 35, Residues 215, Estimated correctness of the model 38.2 % 8 chains (59 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 5714 restraints for refining 2851 atoms. 4697 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2440 (Rfree = 0.000) for 2851 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.2256 (Rfree = 0.000) for 2811 atoms. Found 11 (21 requested) and removed 17 (10 requested) atoms. Cycle 3: After refmac, R = 0.2153 (Rfree = 0.000) for 2789 atoms. Found 5 (21 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.2123 (Rfree = 0.000) for 2763 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2064 (Rfree = 0.000) for 2749 atoms. Found 5 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 2884 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 2923 seeds are put forward Round 1: 194 peptides, 35 chains. Longest chain 11 peptides. Score 0.394 Round 2: 232 peptides, 33 chains. Longest chain 27 peptides. Score 0.554 Round 3: 226 peptides, 33 chains. Longest chain 20 peptides. Score 0.535 Round 4: 229 peptides, 35 chains. Longest chain 21 peptides. Score 0.517 Round 5: 226 peptides, 34 chains. Longest chain 17 peptides. Score 0.521 Taking the results from Round 2 Chains 33, Residues 199, Estimated correctness of the model 13.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6445 restraints for refining 2852 atoms. 5682 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2029 (Rfree = 0.000) for 2852 atoms. Found 19 (21 requested) and removed 17 (10 requested) atoms. Cycle 7: After refmac, R = 0.1825 (Rfree = 0.000) for 2838 atoms. Found 11 (21 requested) and removed 12 (10 requested) atoms. Cycle 8: After refmac, R = 0.1774 (Rfree = 0.000) for 2832 atoms. Found 5 (21 requested) and removed 15 (10 requested) atoms. Cycle 9: After refmac, R = 0.1670 (Rfree = 0.000) for 2815 atoms. Found 4 (21 requested) and removed 15 (10 requested) atoms. Cycle 10: After refmac, R = 0.1677 (Rfree = 0.000) for 2802 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2966 seeds are put forward Round 1: 184 peptides, 31 chains. Longest chain 11 peptides. Score 0.420 Round 2: 220 peptides, 34 chains. Longest chain 25 peptides. Score 0.502 Round 3: 222 peptides, 34 chains. Longest chain 13 peptides. Score 0.508 Round 4: 218 peptides, 32 chains. Longest chain 16 peptides. Score 0.524 Round 5: 205 peptides, 32 chains. Longest chain 14 peptides. Score 0.480 Taking the results from Round 4 Chains 32, Residues 186, Estimated correctness of the model 1.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6571 restraints for refining 2851 atoms. 5859 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1995 (Rfree = 0.000) for 2851 atoms. Found 19 (21 requested) and removed 20 (10 requested) atoms. Cycle 12: After refmac, R = 0.1825 (Rfree = 0.000) for 2843 atoms. Found 7 (21 requested) and removed 18 (10 requested) atoms. Cycle 13: After refmac, R = 0.2001 (Rfree = 0.000) for 2823 atoms. Found 20 (21 requested) and removed 15 (10 requested) atoms. Cycle 14: After refmac, R = 0.1848 (Rfree = 0.000) for 2827 atoms. Found 14 (21 requested) and removed 20 (10 requested) atoms. Cycle 15: After refmac, R = 0.1699 (Rfree = 0.000) for 2813 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2962 seeds are put forward Round 1: 180 peptides, 32 chains. Longest chain 11 peptides. Score 0.389 Round 2: 218 peptides, 33 chains. Longest chain 15 peptides. Score 0.509 Round 3: 223 peptides, 28 chains. Longest chain 24 peptides. Score 0.594 Round 4: 218 peptides, 32 chains. Longest chain 15 peptides. Score 0.524 Round 5: 221 peptides, 34 chains. Longest chain 17 peptides. Score 0.505 Taking the results from Round 3 Chains 30, Residues 195, Estimated correctness of the model 26.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5885 reflections ( 99.85 % complete ) and 6218 restraints for refining 2852 atoms. 5429 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1929 (Rfree = 0.000) for 2852 atoms. Found 14 (21 requested) and removed 21 (10 requested) atoms. Cycle 17: After refmac, R = 0.1755 (Rfree = 0.000) for 2836 atoms. Found 9 (21 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1691 (Rfree = 0.000) for 2829 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.1620 (Rfree = 0.000) for 2821 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.1550 (Rfree = 0.000) for 2820 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2979 seeds are put forward Round 1: 169 peptides, 30 chains. Longest chain 15 peptides. Score 0.379 Round 2: 201 peptides, 32 chains. Longest chain 16 peptides. Score 0.466 Round 3: 185 peptides, 30 chains. Longest chain 13 peptides. Score 0.440 Round 4: 182 peptides, 31 chains. Longest chain 10 peptides. Score 0.413 Round 5: 192 peptides, 31 chains. Longest chain 20 peptides. Score 0.450 Taking the results from Round 2 Chains 32, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6546 restraints for refining 2852 atoms. 5902 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1776 (Rfree = 0.000) for 2852 atoms. Found 11 (21 requested) and removed 10 (10 requested) atoms. Cycle 22: After refmac, R = 0.1717 (Rfree = 0.000) for 2848 atoms. Found 13 (21 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.1686 (Rfree = 0.000) for 2848 atoms. Found 8 (21 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1572 (Rfree = 0.000) for 2843 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1591 (Rfree = 0.000) for 2837 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 2995 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3011 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 10 peptides. Score 0.315 Round 2: 217 peptides, 36 chains. Longest chain 14 peptides. Score 0.462 Round 3: 189 peptides, 30 chains. Longest chain 12 peptides. Score 0.455 Round 4: 184 peptides, 31 chains. Longest chain 14 peptides. Score 0.420 Round 5: 191 peptides, 30 chains. Longest chain 13 peptides. Score 0.462 Taking the results from Round 5 Chains 30, Residues 161, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6537 restraints for refining 2850 atoms. 5911 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1852 (Rfree = 0.000) for 2850 atoms. Found 15 (21 requested) and removed 12 (10 requested) atoms. Cycle 27: After refmac, R = 0.1689 (Rfree = 0.000) for 2847 atoms. Found 16 (21 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1571 (Rfree = 0.000) for 2852 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.1572 (Rfree = 0.000) for 2840 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1548 (Rfree = 0.000) for 2832 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2984 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3000 seeds are put forward Round 1: 167 peptides, 30 chains. Longest chain 15 peptides. Score 0.372 Round 2: 192 peptides, 30 chains. Longest chain 16 peptides. Score 0.465 Round 3: 190 peptides, 29 chains. Longest chain 12 peptides. Score 0.474 Round 4: 204 peptides, 29 chains. Longest chain 28 peptides. Score 0.521 Round 5: 193 peptides, 29 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 4 Chains 32, Residues 175, Estimated correctness of the model 0.8 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6161 restraints for refining 2852 atoms. 5374 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2049 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 32: After refmac, R = 0.1878 (Rfree = 0.000) for 2844 atoms. Found 11 (21 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.1821 (Rfree = 0.000) for 2839 atoms. Found 7 (21 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.1860 (Rfree = 0.000) for 2830 atoms. Found 15 (21 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 2831 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2988 seeds are put forward Round 1: 171 peptides, 33 chains. Longest chain 11 peptides. Score 0.337 Round 2: 184 peptides, 28 chains. Longest chain 14 peptides. Score 0.468 Round 3: 191 peptides, 29 chains. Longest chain 15 peptides. Score 0.477 Round 4: 202 peptides, 30 chains. Longest chain 15 peptides. Score 0.500 Round 5: 207 peptides, 31 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6223 restraints for refining 2851 atoms. 5488 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2074 (Rfree = 0.000) for 2851 atoms. Found 17 (21 requested) and removed 17 (10 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 2839 atoms. Found 16 (21 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.1853 (Rfree = 0.000) for 2829 atoms. Found 14 (21 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.1556 (Rfree = 0.000) for 2823 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.1803 (Rfree = 0.000) for 2811 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward NCS extension: 0 residues added, 2929 seeds are put forward Round 1: 166 peptides, 35 chains. Longest chain 15 peptides. Score 0.281 Round 2: 183 peptides, 30 chains. Longest chain 14 peptides. Score 0.433 Round 3: 183 peptides, 32 chains. Longest chain 12 peptides. Score 0.400 Round 4: 186 peptides, 29 chains. Longest chain 18 peptides. Score 0.459 Round 5: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 4 Chains 29, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6557 restraints for refining 2852 atoms. 5958 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2145 (Rfree = 0.000) for 2852 atoms. Found 17 (21 requested) and removed 15 (10 requested) atoms. Cycle 42: After refmac, R = 0.2068 (Rfree = 0.000) for 2842 atoms. Found 18 (21 requested) and removed 16 (10 requested) atoms. Cycle 43: After refmac, R = 0.1901 (Rfree = 0.000) for 2843 atoms. Found 19 (21 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.1504 (Rfree = 0.000) for 2842 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1654 (Rfree = 0.000) for 2839 atoms. Found 11 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3000 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 12 peptides. Score 0.305 Round 2: 178 peptides, 33 chains. Longest chain 10 peptides. Score 0.365 Round 3: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.395 Round 4: 180 peptides, 33 chains. Longest chain 13 peptides. Score 0.372 Round 5: 179 peptides, 32 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 143, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5885 reflections ( 99.85 % complete ) and 6505 restraints for refining 2851 atoms. 5940 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1884 (Rfree = 0.000) for 2851 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1816 (Rfree = 0.000) for 2837 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1748 (Rfree = 0.000) for 2825 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1685 (Rfree = 0.000) for 2812 atoms. TimeTaking 55.65