Mon 24 Dec 07:29:23 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fur-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:29:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-3.6-parrot-noncs/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-noncs.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-noncs.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 3688 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3287 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3016 (Rfree = 0.000) for 3688 atoms. Found 17 (23 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 3726 seeds are put forward NCS extension: 0 residues added, 3726 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 8 peptides. Score 0.287 Round 2: 215 peptides, 37 chains. Longest chain 12 peptides. Score 0.446 Round 3: 236 peptides, 34 chains. Longest chain 15 peptides. Score 0.560 Round 4: 241 peptides, 32 chains. Longest chain 15 peptides. Score 0.602 Round 5: 236 peptides, 30 chains. Longest chain 18 peptides. Score 0.613 Taking the results from Round 5 Chains 32, Residues 206, Estimated correctness of the model 19.7 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6857 restraints for refining 3031 atoms. 6008 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2390 (Rfree = 0.000) for 3031 atoms. Found 13 (19 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2226 (Rfree = 0.000) for 2962 atoms. Found 11 (19 requested) and removed 19 (9 requested) atoms. Cycle 3: After refmac, R = 0.2138 (Rfree = 0.000) for 2924 atoms. Found 11 (18 requested) and removed 16 (9 requested) atoms. Cycle 4: After refmac, R = 0.2083 (Rfree = 0.000) for 2899 atoms. Found 5 (18 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2100 (Rfree = 0.000) for 2878 atoms. Found 9 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 3012 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3026 seeds are put forward Round 1: 162 peptides, 28 chains. Longest chain 10 peptides. Score 0.390 Round 2: 195 peptides, 31 chains. Longest chain 14 peptides. Score 0.467 Round 3: 196 peptides, 30 chains. Longest chain 18 peptides. Score 0.486 Round 4: 204 peptides, 31 chains. Longest chain 14 peptides. Score 0.498 Round 5: 212 peptides, 30 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 5 Chains 30, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6960 restraints for refining 2968 atoms. 6262 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2086 (Rfree = 0.000) for 2968 atoms. Found 11 (19 requested) and removed 23 (9 requested) atoms. Cycle 7: After refmac, R = 0.1848 (Rfree = 0.000) for 2936 atoms. Found 8 (18 requested) and removed 21 (9 requested) atoms. Cycle 8: After refmac, R = 0.1810 (Rfree = 0.000) for 2911 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 9: After refmac, R = 0.1699 (Rfree = 0.000) for 2893 atoms. Found 7 (18 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.1681 (Rfree = 0.000) for 2877 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 2983 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3004 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 9 peptides. Score 0.393 Round 2: 201 peptides, 32 chains. Longest chain 12 peptides. Score 0.473 Round 3: 219 peptides, 34 chains. Longest chain 15 peptides. Score 0.505 Round 4: 209 peptides, 34 chains. Longest chain 13 peptides. Score 0.470 Round 5: 219 peptides, 31 chains. Longest chain 29 peptides. Score 0.548 Taking the results from Round 5 Chains 31, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6910 restraints for refining 3024 atoms. 6189 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1936 (Rfree = 0.000) for 3024 atoms. Found 14 (19 requested) and removed 25 (9 requested) atoms. Cycle 12: After refmac, R = 0.1874 (Rfree = 0.000) for 2989 atoms. Found 8 (19 requested) and removed 15 (9 requested) atoms. Cycle 13: After refmac, R = 0.1843 (Rfree = 0.000) for 2969 atoms. Found 12 (19 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1797 (Rfree = 0.000) for 2955 atoms. Found 12 (19 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.1801 (Rfree = 0.000) for 2949 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3032 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 3070 seeds are put forward Round 1: 167 peptides, 35 chains. Longest chain 8 peptides. Score 0.288 Round 2: 198 peptides, 32 chains. Longest chain 14 peptides. Score 0.462 Round 3: 191 peptides, 30 chains. Longest chain 14 peptides. Score 0.468 Round 4: 190 peptides, 30 chains. Longest chain 18 peptides. Score 0.464 Round 5: 208 peptides, 28 chains. Longest chain 18 peptides. Score 0.556 Taking the results from Round 5 Chains 28, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6819 restraints for refining 3005 atoms. 6127 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1875 (Rfree = 0.000) for 3005 atoms. Found 14 (19 requested) and removed 21 (9 requested) atoms. Cycle 17: After refmac, R = 0.1734 (Rfree = 0.000) for 2986 atoms. Found 10 (19 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.1787 (Rfree = 0.000) for 2974 atoms. Found 13 (19 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.1804 (Rfree = 0.000) for 2963 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1828 (Rfree = 0.000) for 2955 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3082 seeds are put forward Round 1: 173 peptides, 33 chains. Longest chain 12 peptides. Score 0.349 Round 2: 187 peptides, 32 chains. Longest chain 16 peptides. Score 0.421 Round 3: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.463 Round 4: 191 peptides, 29 chains. Longest chain 17 peptides. Score 0.484 Round 5: 189 peptides, 30 chains. Longest chain 12 peptides. Score 0.461 Taking the results from Round 4 Chains 30, Residues 162, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6890 restraints for refining 3032 atoms. 6226 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1970 (Rfree = 0.000) for 3032 atoms. Found 11 (19 requested) and removed 17 (9 requested) atoms. Cycle 22: After refmac, R = 0.1806 (Rfree = 0.000) for 3009 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.1829 (Rfree = 0.000) for 2988 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.1819 (Rfree = 0.000) for 2981 atoms. Found 13 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1431 (Rfree = 0.000) for 2977 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 3025 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 3061 seeds are put forward Round 1: 155 peptides, 29 chains. Longest chain 14 peptides. Score 0.344 Round 2: 188 peptides, 34 chains. Longest chain 16 peptides. Score 0.392 Round 3: 184 peptides, 29 chains. Longest chain 22 peptides. Score 0.458 Round 4: 185 peptides, 29 chains. Longest chain 19 peptides. Score 0.462 Round 5: 187 peptides, 30 chains. Longest chain 18 peptides. Score 0.453 Taking the results from Round 4 Chains 29, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 7131 restraints for refining 3032 atoms. 6536 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1869 (Rfree = 0.000) for 3032 atoms. Found 7 (19 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.2086 (Rfree = 0.000) for 3016 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 28: After refmac, R = 0.1891 (Rfree = 0.000) for 3007 atoms. Found 17 (19 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.1794 (Rfree = 0.000) for 3002 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1662 (Rfree = 0.000) for 2991 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.81 Search for helices and strands: 0 residues in 0 chains, 3100 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3127 seeds are put forward Round 1: 130 peptides, 26 chains. Longest chain 12 peptides. Score 0.291 Round 2: 149 peptides, 27 chains. Longest chain 14 peptides. Score 0.355 Round 3: 157 peptides, 27 chains. Longest chain 16 peptides. Score 0.388 Round 4: 170 peptides, 27 chains. Longest chain 20 peptides. Score 0.439 Round 5: 175 peptides, 29 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 4 Chains 27, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 7174 restraints for refining 3031 atoms. 6629 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1811 (Rfree = 0.000) for 3031 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. Cycle 32: After refmac, R = 0.2606 (Rfree = 0.000) for 3023 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 33: After refmac, R = 0.1910 (Rfree = 0.000) for 2996 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.1776 (Rfree = 0.000) for 2986 atoms. Found 13 (19 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1718 (Rfree = 0.000) for 2981 atoms. Found 15 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 3088 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3122 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 7 peptides. Score 0.258 Round 2: 148 peptides, 28 chains. Longest chain 8 peptides. Score 0.333 Round 3: 146 peptides, 28 chains. Longest chain 8 peptides. Score 0.324 Round 4: 150 peptides, 26 chains. Longest chain 10 peptides. Score 0.377 Round 5: 152 peptides, 27 chains. Longest chain 10 peptides. Score 0.367 Taking the results from Round 4 Chains 26, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 7028 restraints for refining 2994 atoms. 6558 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1671 (Rfree = 0.000) for 2994 atoms. Found 10 (19 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.1563 (Rfree = 0.000) for 2975 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.1943 (Rfree = 0.000) for 2970 atoms. Found 17 (19 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.1527 (Rfree = 0.000) for 2961 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1553 (Rfree = 0.000) for 2956 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 3030 seeds are put forward NCS extension: 0 residues added, 3030 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 12 peptides. Score 0.310 Round 2: 152 peptides, 30 chains. Longest chain 9 peptides. Score 0.314 Round 3: 164 peptides, 28 chains. Longest chain 11 peptides. Score 0.398 Round 4: 157 peptides, 26 chains. Longest chain 18 peptides. Score 0.405 Round 5: 175 peptides, 31 chains. Longest chain 12 peptides. Score 0.391 Taking the results from Round 4 Chains 26, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5038 reflections ( 99.58 % complete ) and 6995 restraints for refining 2994 atoms. 6497 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1819 (Rfree = 0.000) for 2994 atoms. Found 13 (19 requested) and removed 26 (9 requested) atoms. Cycle 42: After refmac, R = 0.1843 (Rfree = 0.000) for 2968 atoms. Found 18 (19 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.1686 (Rfree = 0.000) for 2965 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.1641 (Rfree = 0.000) for 2959 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 45: After refmac, R = 0.1227 (Rfree = 0.000) for 2956 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 3024 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3047 seeds are put forward Round 1: 123 peptides, 27 chains. Longest chain 8 peptides. Score 0.240 Round 2: 154 peptides, 29 chains. Longest chain 11 peptides. Score 0.340 Round 3: 153 peptides, 28 chains. Longest chain 12 peptides. Score 0.354 Round 4: 154 peptides, 29 chains. Longest chain 11 peptides. Score 0.340 Round 5: 163 peptides, 29 chains. Longest chain 12 peptides. Score 0.377 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 134, 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 6953 restraints for refining 3006 atoms. 6446 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2020 (Rfree = 0.000) for 3006 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1960 (Rfree = 0.000) for 2986 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1747 (Rfree = 0.000) for 2970 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1713 (Rfree = 0.000) for 2958 atoms. TimeTaking 34.23