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 1vjv-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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/1vjv-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 19:28:04 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/1vjv-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-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 304 and 0 Target number of residues in the AU: 304 Target solvent content: 0.6207 Checking the provided sequence file Detected sequence length: 415 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 415 Adjusted target solvent content: 0.48 Input MTZ file: 1vjv-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: 19 Cell parameters: 49.299 81.862 107.491 90.000 90.000 90.000 Input sequence file: 1vjv-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3320 target number of atoms Had to go as low as 0.55 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: 65.126 3.800 Wilson plot Bfac: 61.51 4448 reflections ( 96.55 % complete ) and 0 restraints for refining 3669 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3037 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3074 (Rfree = 0.000) for 3669 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 3722 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 7 peptides. Score 0.248 Round 2: 193 peptides, 31 chains. Longest chain 14 peptides. Score 0.446 Round 3: 200 peptides, 31 chains. Longest chain 16 peptides. Score 0.470 Round 4: 190 peptides, 28 chains. Longest chain 15 peptides. Score 0.481 Round 5: 199 peptides, 27 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 5 Chains 28, Residues 172, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4448 reflections ( 96.55 % complete ) and 7117 restraints for refining 3002 atoms. 6416 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2778 (Rfree = 0.000) for 3002 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 2: After refmac, R = 0.2563 (Rfree = 0.000) for 2908 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 3: After refmac, R = 0.2266 (Rfree = 0.000) for 2864 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2255 (Rfree = 0.000) for 2839 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 5: After refmac, R = 0.2237 (Rfree = 0.000) for 2824 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward Round 1: 173 peptides, 32 chains. Longest chain 11 peptides. Score 0.357 Round 2: 214 peptides, 31 chains. Longest chain 16 peptides. Score 0.516 Round 3: 226 peptides, 32 chains. Longest chain 17 peptides. Score 0.540 Round 4: 220 peptides, 32 chains. Longest chain 14 peptides. Score 0.521 Round 5: 225 peptides, 30 chains. Longest chain 22 peptides. Score 0.563 Taking the results from Round 5 Chains 32, Residues 195, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4448 reflections ( 96.55 % complete ) and 6400 restraints for refining 2862 atoms. 5624 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2137 (Rfree = 0.000) for 2862 atoms. Found 11 (15 requested) and removed 43 (7 requested) atoms. Cycle 7: After refmac, R = 0.2170 (Rfree = 0.000) for 2808 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1946 (Rfree = 0.000) for 2773 atoms. Found 11 (15 requested) and removed 15 (7 requested) atoms. Cycle 9: After refmac, R = 0.1909 (Rfree = 0.000) for 2758 atoms. Found 14 (15 requested) and removed 17 (7 requested) atoms. Cycle 10: After refmac, R = 0.1842 (Rfree = 0.000) for 2748 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 2885 seeds are put forward Round 1: 204 peptides, 34 chains. Longest chain 16 peptides. Score 0.439 Round 2: 220 peptides, 29 chains. Longest chain 22 peptides. Score 0.562 Round 3: 211 peptides, 27 chains. Longest chain 25 peptides. Score 0.562 Round 4: 205 peptides, 27 chains. Longest chain 20 peptides. Score 0.544 Round 5: 201 peptides, 28 chains. Longest chain 19 peptides. Score 0.517 Taking the results from Round 3 Chains 28, Residues 184, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4448 reflections ( 96.55 % complete ) and 6327 restraints for refining 2890 atoms. 5532 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2248 (Rfree = 0.000) for 2890 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 12: After refmac, R = 0.2097 (Rfree = 0.000) for 2850 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1959 (Rfree = 0.000) for 2835 atoms. Found 12 (15 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.1952 (Rfree = 0.000) for 2819 atoms. Found 13 (15 requested) and removed 18 (7 requested) atoms. Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 2808 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 2886 seeds are put forward Round 1: 188 peptides, 32 chains. Longest chain 15 peptides. Score 0.413 Round 2: 199 peptides, 27 chains. Longest chain 25 peptides. Score 0.525 Round 3: 205 peptides, 30 chains. Longest chain 18 peptides. Score 0.501 Round 4: 212 peptides, 28 chains. Longest chain 24 peptides. Score 0.551 Round 5: 217 peptides, 29 chains. Longest chain 23 peptides. Score 0.553 Taking the results from Round 5 Chains 30, Residues 188, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4448 reflections ( 96.55 % complete ) and 6438 restraints for refining 2900 atoms. 5675 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2525 (Rfree = 0.000) for 2900 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 17: After refmac, R = 0.2282 (Rfree = 0.000) for 2847 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 18: After refmac, R = 0.2081 (Rfree = 0.000) for 2818 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.2093 (Rfree = 0.000) for 2808 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 20: After refmac, R = 0.1966 (Rfree = 0.000) for 2791 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 2885 seeds are put forward Round 1: 147 peptides, 29 chains. Longest chain 10 peptides. Score 0.304 Round 2: 185 peptides, 31 chains. Longest chain 15 peptides. Score 0.417 Round 3: 204 peptides, 31 chains. Longest chain 20 peptides. Score 0.484 Round 4: 202 peptides, 31 chains. Longest chain 20 peptides. Score 0.477 Round 5: 197 peptides, 29 chains. Longest chain 21 peptides. Score 0.490 Taking the results from Round 5 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4448 reflections ( 96.55 % complete ) and 6592 restraints for refining 2891 atoms. 5909 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2169 (Rfree = 0.000) for 2891 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 22: After refmac, R = 0.2083 (Rfree = 0.000) for 2870 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1887 (Rfree = 0.000) for 2857 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 24: After refmac, R = 0.1893 (Rfree = 0.000) for 2845 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1538 (Rfree = 0.000) for 2841 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward Round 1: 166 peptides, 32 chains. Longest chain 20 peptides. Score 0.329 Round 2: 194 peptides, 36 chains. Longest chain 15 peptides. Score 0.372 Round 3: 196 peptides, 31 chains. Longest chain 21 peptides. Score 0.456 Round 4: 196 peptides, 34 chains. Longest chain 17 peptides. Score 0.411 Round 5: 211 peptides, 35 chains. Longest chain 17 peptides. Score 0.448 Taking the results from Round 3 Chains 31, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4448 reflections ( 96.55 % complete ) and 6635 restraints for refining 2870 atoms. 6006 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2272 (Rfree = 0.000) for 2870 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 27: After refmac, R = 0.2131 (Rfree = 0.000) for 2851 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 28: After refmac, R = 0.2022 (Rfree = 0.000) for 2847 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.1901 (Rfree = 0.000) for 2846 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.1480 (Rfree = 0.000) for 2842 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 10 peptides. Score 0.277 Round 2: 163 peptides, 28 chains. Longest chain 16 peptides. Score 0.384 Round 3: 169 peptides, 29 chains. Longest chain 15 peptides. Score 0.390 Round 4: 164 peptides, 27 chains. Longest chain 15 peptides. Score 0.404 Round 5: 183 peptides, 32 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 4 Chains 27, Residues 137, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4448 reflections ( 96.55 % complete ) and 6856 restraints for refining 2906 atoms. 6319 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1989 (Rfree = 0.000) for 2906 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 32: After refmac, R = 0.2194 (Rfree = 0.000) for 2898 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 33: After refmac, R = 0.1576 (Rfree = 0.000) for 2889 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1440 (Rfree = 0.000) for 2877 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1394 (Rfree = 0.000) for 2871 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward Round 1: 155 peptides, 34 chains. Longest chain 11 peptides. Score 0.250 Round 2: 164 peptides, 28 chains. Longest chain 15 peptides. Score 0.388 Round 3: 168 peptides, 28 chains. Longest chain 15 peptides. Score 0.403 Round 4: 171 peptides, 26 chains. Longest chain 16 peptides. Score 0.446 Round 5: 180 peptides, 28 chains. Longest chain 18 peptides. Score 0.446 Taking the results from Round 5 Chains 28, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4448 reflections ( 96.55 % complete ) and 7110 restraints for refining 3003 atoms. 6530 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2156 (Rfree = 0.000) for 3003 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 37: After refmac, R = 0.2156 (Rfree = 0.000) for 2972 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 38: After refmac, R = 0.1927 (Rfree = 0.000) for 2951 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2009 (Rfree = 0.000) for 2940 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1568 (Rfree = 0.000) for 2929 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 3007 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 10 peptides. Score 0.251 Round 2: 150 peptides, 29 chains. Longest chain 12 peptides. Score 0.316 Round 3: 154 peptides, 27 chains. Longest chain 12 peptides. Score 0.366 Round 4: 165 peptides, 30 chains. Longest chain 12 peptides. Score 0.359 Round 5: 169 peptides, 31 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 3 Chains 27, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4448 reflections ( 96.55 % complete ) and 7108 restraints for refining 2937 atoms. 6627 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2171 (Rfree = 0.000) for 2937 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2030 (Rfree = 0.000) for 2922 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2029 (Rfree = 0.000) for 2909 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2229 (Rfree = 0.000) for 2903 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 45: After refmac, R = 0.2299 (Rfree = 0.000) for 2900 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 2982 seeds are put forward Round 1: 99 peptides, 23 chains. Longest chain 6 peptides. Score 0.202 Round 2: 119 peptides, 19 chains. Longest chain 20 peptides. Score 0.367 Round 3: 111 peptides, 20 chains. Longest chain 15 peptides. Score 0.315 Round 4: 107 peptides, 17 chains. Longest chain 16 peptides. Score 0.355 Round 5: 113 peptides, 18 chains. Longest chain 20 peptides. Score 0.361 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 100, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vjv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4448 reflections ( 96.55 % complete ) and 6707 restraints for refining 2832 atoms. 6304 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2524 (Rfree = 0.000) for 2832 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2152 (Rfree = 0.000) for 2809 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2000 (Rfree = 0.000) for 2795 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1984 (Rfree = 0.000) for 2782 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 51.49