Tue 25 Dec 19:27:55 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 2ogi-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.8-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/2ogi-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.8-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 ============================================================ Tue 25 Dec 19:28:05 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/2ogi-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.8-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 271 and 0 Target number of residues in the AU: 271 Target solvent content: 0.6680 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-3.8-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-3.8-parrot-hancs.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 3.800 Wilson plot Bfac: 90.13 4427 reflections ( 99.77 % complete ) and 0 restraints for refining 3458 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3605 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 3458 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 3558 seeds are put forward NCS extension: 0 residues added, 3558 seeds are put forward Round 1: 147 peptides, 29 chains. Longest chain 12 peptides. Score 0.302 Round 2: 189 peptides, 30 chains. Longest chain 13 peptides. Score 0.443 Round 3: 197 peptides, 33 chains. Longest chain 16 peptides. Score 0.426 Round 4: 199 peptides, 31 chains. Longest chain 14 peptides. Score 0.463 Round 5: 198 peptides, 31 chains. Longest chain 13 peptides. Score 0.459 Taking the results from Round 4 Chains 31, Residues 168, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6660 restraints for refining 2836 atoms. 5988 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2354 (Rfree = 0.000) for 2836 atoms. Found 6 (15 requested) and removed 29 (7 requested) atoms. Cycle 2: After refmac, R = 0.2130 (Rfree = 0.000) for 2773 atoms. Found 4 (15 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.2033 (Rfree = 0.000) for 2749 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.1939 (Rfree = 0.000) for 2738 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2040 (Rfree = 0.000) for 2726 atoms. Found 8 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 2872 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2889 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 13 peptides. Score 0.370 Round 2: 195 peptides, 29 chains. Longest chain 18 peptides. Score 0.479 Round 3: 207 peptides, 32 chains. Longest chain 13 peptides. Score 0.475 Round 4: 216 peptides, 31 chains. Longest chain 13 peptides. Score 0.518 Round 5: 208 peptides, 27 chains. Longest chain 25 peptides. Score 0.548 Taking the results from Round 5 Chains 28, Residues 181, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6305 restraints for refining 2835 atoms. 5534 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2329 (Rfree = 0.000) for 2835 atoms. Found 11 (15 requested) and removed 35 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2191 (Rfree = 0.000) for 2796 atoms. Found 9 (15 requested) and removed 22 (7 requested) atoms. Cycle 8: After refmac, R = 0.2145 (Rfree = 0.000) for 2775 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. Cycle 9: After refmac, R = 0.1886 (Rfree = 0.000) for 2764 atoms. Found 1 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1893 (Rfree = 0.000) for 2750 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 2845 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2863 seeds are put forward Round 1: 161 peptides, 30 chains. Longest chain 9 peptides. Score 0.340 Round 2: 175 peptides, 27 chains. Longest chain 14 peptides. Score 0.440 Round 3: 189 peptides, 28 chains. Longest chain 14 peptides. Score 0.473 Round 4: 182 peptides, 27 chains. Longest chain 14 peptides. Score 0.465 Round 5: 184 peptides, 26 chains. Longest chain 15 peptides. Score 0.486 Taking the results from Round 5 Chains 26, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4427 reflections ( 99.77 % complete ) and 6592 restraints for refining 2836 atoms. 5986 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2055 (Rfree = 0.000) for 2836 atoms. Found 14 (15 requested) and removed 20 (7 requested) atoms. Cycle 12: After refmac, R = 0.2109 (Rfree = 0.000) for 2814 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 13: After refmac, R = 0.1809 (Rfree = 0.000) for 2807 atoms. Found 5 (15 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1893 (Rfree = 0.000) for 2786 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.2049 (Rfree = 0.000) for 2779 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 2878 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2898 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 9 peptides. Score 0.297 Round 2: 156 peptides, 26 chains. Longest chain 11 peptides. Score 0.387 Round 3: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.401 Round 4: 162 peptides, 27 chains. Longest chain 14 peptides. Score 0.393 Round 5: 155 peptides, 24 chains. Longest chain 14 peptides. Score 0.416 Taking the results from Round 5 Chains 24, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6751 restraints for refining 2835 atoms. 6251 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2169 (Rfree = 0.000) for 2835 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2109 (Rfree = 0.000) for 2806 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 18: After refmac, R = 0.2017 (Rfree = 0.000) for 2790 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1628 (Rfree = 0.000) for 2777 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1548 (Rfree = 0.000) for 2763 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 2875 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2892 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.269 Round 2: 166 peptides, 27 chains. Longest chain 12 peptides. Score 0.408 Round 3: 176 peptides, 27 chains. Longest chain 10 peptides. Score 0.444 Round 4: 167 peptides, 27 chains. Longest chain 11 peptides. Score 0.412 Round 5: 167 peptides, 27 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 3 Chains 27, Residues 149, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6041 restraints for refining 2749 atoms. 5450 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1981 (Rfree = 0.000) for 2749 atoms. Found 12 (15 requested) and removed 17 (7 requested) atoms. Cycle 22: After refmac, R = 0.1911 (Rfree = 0.000) for 2731 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.1552 (Rfree = 0.000) for 2727 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1628 (Rfree = 0.000) for 2717 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.1446 (Rfree = 0.000) for 2708 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2817 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 8 peptides. Score 0.264 Round 2: 150 peptides, 23 chains. Longest chain 12 peptides. Score 0.414 Round 3: 148 peptides, 25 chains. Longest chain 14 peptides. Score 0.374 Round 4: 144 peptides, 26 chains. Longest chain 11 peptides. Score 0.341 Round 5: 145 peptides, 27 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 2 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4427 reflections ( 99.77 % complete ) and 6338 restraints for refining 2753 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1797 (Rfree = 0.000) for 2753 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.1949 (Rfree = 0.000) for 2745 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.1750 (Rfree = 0.000) for 2744 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1358 (Rfree = 0.000) for 2739 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1325 (Rfree = 0.000) for 2728 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2831 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2848 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 8 peptides. Score 0.270 Round 2: 142 peptides, 28 chains. Longest chain 8 peptides. Score 0.299 Round 3: 152 peptides, 27 chains. Longest chain 13 peptides. Score 0.355 Round 4: 155 peptides, 29 chains. Longest chain 10 peptides. Score 0.334 Round 5: 146 peptides, 29 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 3 Chains 27, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6269 restraints for refining 2750 atoms. 5796 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2011 (Rfree = 0.000) for 2750 atoms. Found 14 (15 requested) and removed 23 (7 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1779 (Rfree = 0.000) for 2728 atoms. Found 4 (15 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.1943 (Rfree = 0.000) for 2709 atoms. Found 7 (14 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.1434 (Rfree = 0.000) for 2695 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Cycle 35: After refmac, R = 0.1378 (Rfree = 0.000) for 2682 atoms. Found 0 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2810 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 8 peptides. Score 0.234 Round 2: 132 peptides, 26 chains. Longest chain 7 peptides. Score 0.292 Round 3: 132 peptides, 24 chains. Longest chain 9 peptides. Score 0.328 Round 4: 133 peptides, 24 chains. Longest chain 10 peptides. Score 0.332 Round 5: 140 peptides, 26 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 4 Chains 24, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6341 restraints for refining 2739 atoms. 5929 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1979 (Rfree = 0.000) for 2739 atoms. Found 13 (15 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1750 (Rfree = 0.000) for 2724 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.1840 (Rfree = 0.000) for 2715 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1658 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1587 (Rfree = 0.000) for 2704 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2824 seeds are put forward NCS extension: 0 residues added, 2824 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 6 peptides. Score 0.254 Round 2: 116 peptides, 22 chains. Longest chain 8 peptides. Score 0.297 Round 3: 121 peptides, 23 chains. Longest chain 8 peptides. Score 0.300 Round 4: 126 peptides, 25 chains. Longest chain 8 peptides. Score 0.285 Round 5: 133 peptides, 26 chains. Longest chain 12 peptides. Score 0.296 Taking the results from Round 3 Chains 23, Residues 98, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6508 restraints for refining 2772 atoms. 6125 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1864 (Rfree = 0.000) for 2772 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1737 (Rfree = 0.000) for 2759 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1905 (Rfree = 0.000) for 2749 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.1745 (Rfree = 0.000) for 2744 atoms. Found 14 (15 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.1388 (Rfree = 0.000) for 2743 atoms. Found 0 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 2848 seeds are put forward NCS extension: 0 residues added, 2848 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 6 peptides. Score 0.207 Round 2: 110 peptides, 21 chains. Longest chain 10 peptides. Score 0.290 Round 3: 113 peptides, 22 chains. Longest chain 8 peptides. Score 0.284 Round 4: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.321 Round 5: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 103, 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. Failed to save intermediate PDB 4427 reflections ( 99.77 % complete ) and 6293 restraints for refining 2743 atoms. 5904 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1877 (Rfree = 0.000) for 2743 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1898 (Rfree = 0.000) for 2730 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1775 (Rfree = 0.000) for 2720 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1341 (Rfree = 0.000) for 2709 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:17:04 GMT 2018 Job finished. TimeTaking 49.15