Tue 25 Dec 19:27:57 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-4.0-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 19:28:12 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-4.0-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 270 and 0 Target number of residues in the AU: 270 Target solvent content: 0.6554 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3168 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.516 4.001 Wilson plot Bfac: 81.70 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3631 reflections ( 99.62 % complete ) and 0 restraints for refining 3502 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3164 (Rfree = 0.000) for 3502 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 3558 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 11 peptides. Score 0.279 Round 2: 164 peptides, 30 chains. Longest chain 9 peptides. Score 0.358 Round 3: 165 peptides, 27 chains. Longest chain 10 peptides. Score 0.412 Round 4: 163 peptides, 26 chains. Longest chain 11 peptides. Score 0.421 Round 5: 167 peptides, 26 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 5 Chains 26, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3631 reflections ( 99.62 % complete ) and 7044 restraints for refining 2859 atoms. 6506 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2426 (Rfree = 0.000) for 2859 atoms. Found 12 (13 requested) and removed 19 (6 requested) atoms. Cycle 2: After refmac, R = 0.2159 (Rfree = 0.000) for 2822 atoms. Found 5 (13 requested) and removed 19 (6 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2184 (Rfree = 0.000) for 2792 atoms. Found 13 (13 requested) and removed 37 (6 requested) atoms. Cycle 4: After refmac, R = 0.2251 (Rfree = 0.000) for 2752 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 5: After refmac, R = 0.1899 (Rfree = 0.000) for 2727 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.64 Search for helices and strands: 0 residues in 0 chains, 2825 seeds are put forward Round 1: 158 peptides, 31 chains. Longest chain 9 peptides. Score 0.316 Round 2: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.411 Round 3: 177 peptides, 29 chains. Longest chain 11 peptides. Score 0.424 Round 4: 184 peptides, 29 chains. Longest chain 11 peptides. Score 0.450 Round 5: 176 peptides, 26 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 5 Chains 26, Residues 150, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3631 reflections ( 99.62 % complete ) and 6624 restraints for refining 2859 atoms. 5984 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2257 (Rfree = 0.000) for 2859 atoms. Found 5 (13 requested) and removed 30 (6 requested) atoms. Cycle 7: After refmac, R = 0.2038 (Rfree = 0.000) for 2802 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 8: After refmac, R = 0.1803 (Rfree = 0.000) for 2782 atoms. Found 9 (13 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1855 (Rfree = 0.000) for 2764 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1820 (Rfree = 0.000) for 2751 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 8 peptides. Score 0.291 Round 2: 173 peptides, 31 chains. Longest chain 12 peptides. Score 0.376 Round 3: 168 peptides, 27 chains. Longest chain 12 peptides. Score 0.423 Round 4: 174 peptides, 28 chains. Longest chain 15 peptides. Score 0.429 Round 5: 176 peptides, 25 chains. Longest chain 15 peptides. Score 0.484 Taking the results from Round 5 Chains 25, Residues 151, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3631 reflections ( 99.62 % complete ) and 6388 restraints for refining 2861 atoms. 5673 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2037 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 12: After refmac, R = 0.1978 (Rfree = 0.000) for 2841 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1691 (Rfree = 0.000) for 2822 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.1714 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 15: After refmac, R = 0.1845 (Rfree = 0.000) for 2815 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2916 seeds are put forward Round 1: 133 peptides, 26 chains. Longest chain 11 peptides. Score 0.300 Round 2: 151 peptides, 26 chains. Longest chain 14 peptides. Score 0.375 Round 3: 178 peptides, 29 chains. Longest chain 13 peptides. Score 0.428 Round 4: 172 peptides, 26 chains. Longest chain 16 peptides. Score 0.454 Round 5: 174 peptides, 26 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 5 Chains 26, Residues 148, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3631 reflections ( 99.62 % complete ) and 6782 restraints for refining 2861 atoms. 6199 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2156 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.1827 (Rfree = 0.000) for 2837 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.1992 (Rfree = 0.000) for 2820 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 19: After refmac, R = 0.1735 (Rfree = 0.000) for 2806 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1266 (Rfree = 0.000) for 2802 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2905 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 7 peptides. Score 0.273 Round 2: 162 peptides, 28 chains. Longest chain 10 peptides. Score 0.384 Round 3: 156 peptides, 27 chains. Longest chain 11 peptides. Score 0.377 Round 4: 168 peptides, 27 chains. Longest chain 10 peptides. Score 0.423 Round 5: 172 peptides, 26 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 26, Residues 146, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3631 reflections ( 99.62 % complete ) and 6692 restraints for refining 2861 atoms. 6115 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1791 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 22: After refmac, R = 0.1740 (Rfree = 0.000) for 2840 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.1787 (Rfree = 0.000) for 2829 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1807 (Rfree = 0.000) for 2820 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1762 (Rfree = 0.000) for 2809 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 2921 seeds are put forward Round 1: 129 peptides, 29 chains. Longest chain 8 peptides. Score 0.227 Round 2: 166 peptides, 32 chains. Longest chain 10 peptides. Score 0.332 Round 3: 158 peptides, 31 chains. Longest chain 9 peptides. Score 0.316 Round 4: 160 peptides, 29 chains. Longest chain 9 peptides. Score 0.359 Round 5: 142 peptides, 25 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 4 Chains 29, Residues 131, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3631 reflections ( 99.62 % complete ) and 6778 restraints for refining 2861 atoms. 6248 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1948 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1813 (Rfree = 0.000) for 2839 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1235 (Rfree = 0.000) for 2831 atoms. Found 3 (13 requested) and removed 13 (6 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1099 (Rfree = 0.000) for 2818 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.1093 (Rfree = 0.000) for 2804 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 8 peptides. Score 0.272 Round 2: 132 peptides, 25 chains. Longest chain 9 peptides. Score 0.314 Round 3: 152 peptides, 23 chains. Longest chain 11 peptides. Score 0.429 Round 4: 154 peptides, 24 chains. Longest chain 10 peptides. Score 0.420 Round 5: 143 peptides, 23 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 3 Chains 23, Residues 129, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3631 reflections ( 99.62 % complete ) and 6855 restraints for refining 2861 atoms. 6354 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1899 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1914 (Rfree = 0.000) for 2848 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2023 (Rfree = 0.000) for 2837 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1606 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.1862 (Rfree = 0.000) for 2828 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2914 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.244 Round 2: 128 peptides, 26 chains. Longest chain 7 peptides. Score 0.279 Round 3: 127 peptides, 24 chains. Longest chain 8 peptides. Score 0.311 Round 4: 135 peptides, 24 chains. Longest chain 12 peptides. Score 0.345 Round 5: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 4 Chains 24, Residues 111, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3631 reflections ( 99.62 % complete ) and 6826 restraints for refining 2860 atoms. 6393 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1865 (Rfree = 0.000) for 2860 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.1984 (Rfree = 0.000) for 2846 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1979 (Rfree = 0.000) for 2842 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.1820 (Rfree = 0.000) for 2834 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1762 (Rfree = 0.000) for 2823 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 2907 seeds are put forward Round 1: 120 peptides, 28 chains. Longest chain 6 peptides. Score 0.205 Round 2: 138 peptides, 30 chains. Longest chain 7 peptides. Score 0.249 Round 3: 148 peptides, 28 chains. Longest chain 9 peptides. Score 0.328 Round 4: 141 peptides, 27 chains. Longest chain 11 peptides. Score 0.316 Round 5: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.313 Taking the results from Round 3 Chains 28, Residues 120, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3631 reflections ( 99.62 % complete ) and 6671 restraints for refining 2861 atoms. 6179 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1841 (Rfree = 0.000) for 2861 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 42: After refmac, R = 0.1865 (Rfree = 0.000) for 2840 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 43: After refmac, R = 0.1865 (Rfree = 0.000) for 2830 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1855 (Rfree = 0.000) for 2820 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.1625 (Rfree = 0.000) for 2816 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 2897 seeds are put forward Round 1: 114 peptides, 26 chains. Longest chain 8 peptides. Score 0.215 Round 2: 113 peptides, 22 chains. Longest chain 8 peptides. Score 0.288 Round 3: 128 peptides, 24 chains. Longest chain 9 peptides. Score 0.316 Round 4: 118 peptides, 23 chains. Longest chain 8 peptides. Score 0.291 Round 5: 120 peptides, 21 chains. Longest chain 14 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 99, 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 2ozg-4_warpNtrace.pdb as input ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 3631 reflections ( 99.62 % complete ) and 7107 restraints for refining 2861 atoms. 6732 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2069 (Rfree = 0.000) for 2861 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2050 (Rfree = 0.000) for 2836 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2068 (Rfree = 0.000) for 2820 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1856 (Rfree = 0.000) for 2806 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:36:48 GMT 2018 Job finished. TimeTaking 68.86