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 2fur-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fur-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fur-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-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/2fur-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-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/2fur-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-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 256 and 0 Target number of residues in the AU: 256 Target solvent content: 0.6594 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-3.6-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: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.70 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: 55.473 3.600 Wilson plot Bfac: 83.70 5038 reflections ( 99.58 % complete ) and 0 restraints for refining 3720 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3212 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3213 (Rfree = 0.000) for 3720 atoms. Found 12 (23 requested) and removed 37 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.92 Search for helices and strands: 0 residues in 0 chains, 3751 seeds are put forward NCS extension: 0 residues added, 3751 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 12 peptides. Score 0.326 Round 2: 229 peptides, 34 chains. Longest chain 18 peptides. Score 0.538 Round 3: 233 peptides, 32 chains. Longest chain 17 peptides. Score 0.578 Round 4: 249 peptides, 35 chains. Longest chain 17 peptides. Score 0.587 Round 5: 246 peptides, 32 chains. Longest chain 17 peptides. Score 0.616 Taking the results from Round 5 Chains 32, Residues 214, Estimated correctness of the model 20.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6854 restraints for refining 3032 atoms. 6030 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2403 (Rfree = 0.000) for 3032 atoms. Found 7 (19 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2288 (Rfree = 0.000) for 2945 atoms. Found 2 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2222 (Rfree = 0.000) for 2895 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 2866 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.1854 (Rfree = 0.000) for 2845 atoms. Found 1 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2963 seeds are put forward Round 1: 189 peptides, 35 chains. Longest chain 12 peptides. Score 0.379 Round 2: 216 peptides, 31 chains. Longest chain 19 peptides. Score 0.539 Round 3: 226 peptides, 30 chains. Longest chain 20 peptides. Score 0.584 Round 4: 234 peptides, 32 chains. Longest chain 18 peptides. Score 0.581 Round 5: 241 peptides, 33 chains. Longest chain 23 peptides. Score 0.589 Taking the results from Round 5 Chains 33, Residues 208, Estimated correctness of the model 10.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6277 restraints for refining 2831 atoms. 5478 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2107 (Rfree = 0.000) for 2831 atoms. Found 11 (18 requested) and removed 22 (9 requested) atoms. Cycle 7: After refmac, R = 0.1956 (Rfree = 0.000) for 2797 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.1889 (Rfree = 0.000) for 2782 atoms. Found 1 (17 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1841 (Rfree = 0.000) for 2766 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1839 (Rfree = 0.000) for 2752 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 2851 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2876 seeds are put forward Round 1: 198 peptides, 37 chains. Longest chain 11 peptides. Score 0.381 Round 2: 212 peptides, 35 chains. Longest chain 15 peptides. Score 0.466 Round 3: 212 peptides, 35 chains. Longest chain 18 peptides. Score 0.466 Round 4: 224 peptides, 32 chains. Longest chain 18 peptides. Score 0.550 Round 5: 230 peptides, 33 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 5 Chains 33, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6614 restraints for refining 2925 atoms. 5859 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2362 (Rfree = 0.000) for 2925 atoms. Found 11 (18 requested) and removed 21 (9 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 2886 atoms. Found 2 (18 requested) and removed 21 (9 requested) atoms. Cycle 13: After refmac, R = 0.1765 (Rfree = 0.000) for 2850 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. Cycle 14: After refmac, R = 0.1761 (Rfree = 0.000) for 2831 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.1613 (Rfree = 0.000) for 2818 atoms. Found 2 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.79 Search for helices and strands: 0 residues in 0 chains, 2933 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 2958 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 10 peptides. Score 0.308 Round 2: 198 peptides, 35 chains. Longest chain 13 peptides. Score 0.414 Round 3: 188 peptides, 30 chains. Longest chain 14 peptides. Score 0.457 Round 4: 200 peptides, 27 chains. Longest chain 17 peptides. Score 0.544 Round 5: 207 peptides, 28 chains. Longest chain 16 peptides. Score 0.553 Taking the results from Round 5 Chains 29, Residues 179, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5038 reflections ( 99.58 % complete ) and 6387 restraints for refining 2883 atoms. 5670 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1824 (Rfree = 0.000) for 2883 atoms. Found 7 (18 requested) and removed 21 (9 requested) atoms. Cycle 17: After refmac, R = 0.1809 (Rfree = 0.000) for 2857 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. Cycle 18: After refmac, R = 0.2289 (Rfree = 0.000) for 2847 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 19: After refmac, R = 0.1643 (Rfree = 0.000) for 2833 atoms. Found 10 (18 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1680 (Rfree = 0.000) for 2828 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2937 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 11 peptides. Score 0.348 Round 2: 195 peptides, 31 chains. Longest chain 16 peptides. Score 0.467 Round 3: 193 peptides, 27 chains. Longest chain 21 peptides. Score 0.521 Round 4: 199 peptides, 30 chains. Longest chain 16 peptides. Score 0.496 Round 5: 204 peptides, 31 chains. Longest chain 25 peptides. Score 0.498 Taking the results from Round 3 Chains 27, Residues 166, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5038 reflections ( 99.58 % complete ) and 6532 restraints for refining 2934 atoms. 5849 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1764 (Rfree = 0.000) for 2934 atoms. Found 14 (18 requested) and removed 24 (9 requested) atoms. Cycle 22: After refmac, R = 0.1663 (Rfree = 0.000) for 2910 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. Cycle 23: After refmac, R = 0.1969 (Rfree = 0.000) for 2895 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 24: After refmac, R = 0.1587 (Rfree = 0.000) for 2884 atoms. Found 12 (18 requested) and removed 16 (9 requested) atoms. Cycle 25: After refmac, R = 0.1620 (Rfree = 0.000) for 2876 atoms. Found 12 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 2978 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2997 seeds are put forward Round 1: 152 peptides, 33 chains. Longest chain 10 peptides. Score 0.259 Round 2: 180 peptides, 29 chains. Longest chain 16 peptides. Score 0.443 Round 3: 197 peptides, 35 chains. Longest chain 11 peptides. Score 0.410 Round 4: 195 peptides, 31 chains. Longest chain 14 peptides. Score 0.467 Round 5: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 4 Chains 31, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 7172 restraints for refining 3032 atoms. 6547 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1812 (Rfree = 0.000) for 3032 atoms. Found 6 (19 requested) and removed 18 (9 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1704 (Rfree = 0.000) for 3012 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.1701 (Rfree = 0.000) for 3002 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.1677 (Rfree = 0.000) for 2988 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.1631 (Rfree = 0.000) for 2979 atoms. Found 2 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3061 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3074 seeds are put forward Round 1: 148 peptides, 29 chains. Longest chain 12 peptides. Score 0.315 Round 2: 152 peptides, 26 chains. Longest chain 11 peptides. Score 0.385 Round 3: 168 peptides, 26 chains. Longest chain 12 peptides. Score 0.448 Round 4: 164 peptides, 27 chains. Longest chain 11 peptides. Score 0.415 Round 5: 169 peptides, 27 chains. Longest chain 11 peptides. Score 0.435 Taking the results from Round 3 Chains 26, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 7103 restraints for refining 3032 atoms. 6561 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1690 (Rfree = 0.000) for 3032 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 32: After refmac, R = 0.1650 (Rfree = 0.000) for 3030 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. Cycle 33: After refmac, R = 0.1371 (Rfree = 0.000) for 3022 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1328 (Rfree = 0.000) for 3016 atoms. Found 1 (19 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1357 (Rfree = 0.000) for 3006 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3077 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3093 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 12 peptides. Score 0.303 Round 2: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.347 Round 3: 174 peptides, 28 chains. Longest chain 11 peptides. Score 0.437 Round 4: 175 peptides, 29 chains. Longest chain 13 peptides. Score 0.424 Round 5: 177 peptides, 27 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 5 Chains 27, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 7072 restraints for refining 3032 atoms. 6499 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1881 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.1788 (Rfree = 0.000) for 3026 atoms. Found 14 (19 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.1650 (Rfree = 0.000) for 3022 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1406 (Rfree = 0.000) for 3023 atoms. Found 1 (19 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1566 (Rfree = 0.000) for 3009 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3096 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3117 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 7 peptides. Score 0.231 Round 2: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.339 Round 3: 146 peptides, 26 chains. Longest chain 11 peptides. Score 0.360 Round 4: 144 peptides, 23 chains. Longest chain 10 peptides. Score 0.406 Round 5: 152 peptides, 25 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 4 Chains 23, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5038 reflections ( 99.58 % complete ) and 7273 restraints for refining 3032 atoms. 6812 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1810 (Rfree = 0.000) for 3032 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.1705 (Rfree = 0.000) for 3014 atoms. Found 11 (19 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1670 (Rfree = 0.000) for 3008 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.1597 (Rfree = 0.000) for 3007 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.1555 (Rfree = 0.000) for 3002 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 3089 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3098 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 13 peptides. Score 0.277 Round 2: 164 peptides, 29 chains. Longest chain 15 peptides. Score 0.381 Round 3: 148 peptides, 25 chains. Longest chain 15 peptides. Score 0.386 Round 4: 151 peptides, 25 chains. Longest chain 14 peptides. Score 0.399 Round 5: 141 peptides, 24 chains. Longest chain 14 peptides. Score 0.376 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 126, 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 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5038 reflections ( 99.58 % complete ) and 7250 restraints for refining 3032 atoms. 6771 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1624 (Rfree = 0.000) for 3032 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1529 (Rfree = 0.000) for 3016 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1569 (Rfree = 0.000) for 3002 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1441 (Rfree = 0.000) for 2991 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 52.8