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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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/2ozg-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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 19:28:07 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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 275 and 0 Target number of residues in the AU: 275 Target solvent content: 0.6490 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-3.8-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: 155 Cell parameters: 175.031 175.031 71.923 90.000 90.000 120.000 Input sequence file: 2ozg-3.8-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 3.800 Wilson plot Bfac: 76.79 4249 reflections ( 99.67 % complete ) and 0 restraints for refining 3514 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3355 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3055 (Rfree = 0.000) for 3514 atoms. Found 17 (19 requested) and removed 40 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 3564 seeds are put forward Round 1: 158 peptides, 31 chains. Longest chain 8 peptides. Score 0.316 Round 2: 206 peptides, 32 chains. Longest chain 17 peptides. Score 0.481 Round 3: 216 peptides, 33 chains. Longest chain 13 peptides. Score 0.500 Round 4: 223 peptides, 30 chains. Longest chain 20 peptides. Score 0.564 Round 5: 218 peptides, 32 chains. Longest chain 14 peptides. Score 0.520 Taking the results from Round 4 Chains 30, Residues 193, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6433 restraints for refining 2865 atoms. 5673 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2330 (Rfree = 0.000) for 2865 atoms. Found 9 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2132 (Rfree = 0.000) for 2824 atoms. Found 13 (15 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.1985 (Rfree = 0.000) for 2796 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.1775 (Rfree = 0.000) for 2791 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.1448 (Rfree = 0.000) for 2790 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.63 Search for helices and strands: 0 residues in 0 chains, 2899 seeds are put forward Round 1: 168 peptides, 30 chains. Longest chain 10 peptides. Score 0.374 Round 2: 178 peptides, 28 chains. Longest chain 11 peptides. Score 0.444 Round 3: 187 peptides, 28 chains. Longest chain 14 peptides. Score 0.476 Round 4: 191 peptides, 27 chains. Longest chain 17 peptides. Score 0.504 Round 5: 193 peptides, 27 chains. Longest chain 17 peptides. Score 0.511 Taking the results from Round 5 Chains 27, Residues 166, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6650 restraints for refining 2865 atoms. 5936 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2044 (Rfree = 0.000) for 2865 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.1729 (Rfree = 0.000) for 2838 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.1592 (Rfree = 0.000) for 2821 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1580 (Rfree = 0.000) for 2807 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1568 (Rfree = 0.000) for 2796 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.61 Search for helices and strands: 0 residues in 0 chains, 2901 seeds are put forward Round 1: 156 peptides, 27 chains. Longest chain 10 peptides. Score 0.377 Round 2: 183 peptides, 28 chains. Longest chain 12 peptides. Score 0.462 Round 3: 200 peptides, 30 chains. Longest chain 15 peptides. Score 0.490 Round 4: 198 peptides, 30 chains. Longest chain 16 peptides. Score 0.483 Round 5: 193 peptides, 27 chains. Longest chain 17 peptides. Score 0.511 Taking the results from Round 5 Chains 27, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6757 restraints for refining 2865 atoms. 6120 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2023 (Rfree = 0.000) for 2865 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.1644 (Rfree = 0.000) for 2848 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1610 (Rfree = 0.000) for 2836 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.1488 (Rfree = 0.000) for 2831 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1594 (Rfree = 0.000) for 2824 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.60 Search for helices and strands: 0 residues in 0 chains, 2921 seeds are put forward Round 1: 169 peptides, 31 chains. Longest chain 11 peptides. Score 0.361 Round 2: 178 peptides, 28 chains. Longest chain 13 peptides. Score 0.444 Round 3: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.455 Round 4: 198 peptides, 32 chains. Longest chain 13 peptides. Score 0.453 Round 5: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.454 Taking the results from Round 3 Chains 31, Residues 160, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4249 reflections ( 99.67 % complete ) and 6549 restraints for refining 2865 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1907 (Rfree = 0.000) for 2865 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.1742 (Rfree = 0.000) for 2854 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.1567 (Rfree = 0.000) for 2841 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1561 (Rfree = 0.000) for 2830 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1490 (Rfree = 0.000) for 2825 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 10 peptides. Score 0.300 Round 2: 211 peptides, 36 chains. Longest chain 15 peptides. Score 0.438 Round 3: 210 peptides, 37 chains. Longest chain 14 peptides. Score 0.419 Round 4: 196 peptides, 32 chains. Longest chain 18 peptides. Score 0.446 Round 5: 198 peptides, 30 chains. Longest chain 18 peptides. Score 0.483 Taking the results from Round 5 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6514 restraints for refining 2865 atoms. 5789 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1968 (Rfree = 0.000) for 2865 atoms. Found 9 (15 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1831 (Rfree = 0.000) for 2844 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.1765 (Rfree = 0.000) for 2841 atoms. Found 10 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.1672 (Rfree = 0.000) for 2834 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1633 (Rfree = 0.000) for 2827 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.61 Search for helices and strands: 0 residues in 0 chains, 2928 seeds are put forward Round 1: 170 peptides, 33 chains. Longest chain 11 peptides. Score 0.331 Round 2: 187 peptides, 32 chains. Longest chain 11 peptides. Score 0.413 Round 3: 195 peptides, 34 chains. Longest chain 12 peptides. Score 0.411 Round 4: 203 peptides, 36 chains. Longest chain 11 peptides. Score 0.409 Round 5: 204 peptides, 34 chains. Longest chain 17 peptides. Score 0.444 Taking the results from Round 5 Chains 34, Residues 170, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6448 restraints for refining 2865 atoms. 5691 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1946 (Rfree = 0.000) for 2865 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 27: After refmac, R = 0.1699 (Rfree = 0.000) for 2853 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1645 (Rfree = 0.000) for 2844 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.1652 (Rfree = 0.000) for 2840 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1587 (Rfree = 0.000) for 2842 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.61 Search for helices and strands: 0 residues in 0 chains, 2945 seeds are put forward Round 1: 138 peptides, 31 chains. Longest chain 7 peptides. Score 0.231 Round 2: 175 peptides, 33 chains. Longest chain 9 peptides. Score 0.351 Round 3: 185 peptides, 30 chains. Longest chain 11 peptides. Score 0.438 Round 4: 193 peptides, 33 chains. Longest chain 10 peptides. Score 0.419 Round 5: 182 peptides, 30 chains. Longest chain 10 peptides. Score 0.427 Taking the results from Round 3 Chains 30, Residues 155, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6815 restraints for refining 2865 atoms. 6188 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1725 (Rfree = 0.000) for 2865 atoms. Found 9 (15 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.1695 (Rfree = 0.000) for 2852 atoms. Found 10 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1624 (Rfree = 0.000) for 2850 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1560 (Rfree = 0.000) for 2848 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1480 (Rfree = 0.000) for 2840 atoms. Found 12 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 10 peptides. Score 0.309 Round 2: 150 peptides, 27 chains. Longest chain 13 peptides. Score 0.353 Round 3: 161 peptides, 28 chains. Longest chain 10 peptides. Score 0.380 Round 4: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.414 Round 5: 162 peptides, 26 chains. Longest chain 12 peptides. Score 0.417 Taking the results from Round 5 Chains 26, Residues 136, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6613 restraints for refining 2864 atoms. 6021 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1887 (Rfree = 0.000) for 2864 atoms. Found 11 (15 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.1630 (Rfree = 0.000) for 2851 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.1552 (Rfree = 0.000) for 2850 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1541 (Rfree = 0.000) for 2847 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1512 (Rfree = 0.000) for 2847 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 2968 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.262 Round 2: 149 peptides, 28 chains. Longest chain 12 peptides. Score 0.332 Round 3: 158 peptides, 28 chains. Longest chain 12 peptides. Score 0.368 Round 4: 162 peptides, 29 chains. Longest chain 10 peptides. Score 0.367 Round 5: 152 peptides, 24 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Chains 24, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4249 reflections ( 99.67 % complete ) and 6963 restraints for refining 2864 atoms. 6475 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2042 (Rfree = 0.000) for 2864 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.1714 (Rfree = 0.000) for 2863 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1684 (Rfree = 0.000) for 2866 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1601 (Rfree = 0.000) for 2869 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1164 (Rfree = 0.000) for 2871 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 2969 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 9 peptides. Score 0.225 Round 2: 152 peptides, 30 chains. Longest chain 11 peptides. Score 0.309 Round 3: 140 peptides, 26 chains. Longest chain 9 peptides. Score 0.330 Round 4: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.356 Round 5: 138 peptides, 26 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 117, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2ozg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4249 reflections ( 99.67 % complete ) and 6992 restraints for refining 2864 atoms. 6536 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1800 (Rfree = 0.000) for 2864 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1635 (Rfree = 0.000) for 2844 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1566 (Rfree = 0.000) for 2832 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1667 (Rfree = 0.000) for 2819 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:28:02 GMT 2018 Job finished. TimeTaking 60.07