null Mon 24 Dec 00:24:22 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zkg-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.6-parrot-mrncs ############### 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 00:24:27 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.6-parrot-mrncs/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 308 and 0 Target number of residues in the AU: 308 Target solvent content: 0.6578 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-3.6-parrot-mrncs.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: 4 Cell parameters: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3392 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 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: 29.148 3.600 Wilson plot Bfac: 82.94 5619 reflections ( 99.79 % complete ) and 0 restraints for refining 3759 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3128 (Rfree = 0.000) for 3759 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 3874 seeds are put forward NCS extension: 0 residues added, 3874 seeds are put forward Round 1: 180 peptides, 34 chains. Longest chain 12 peptides. Score 0.335 Round 2: 223 peptides, 33 chains. Longest chain 13 peptides. Score 0.489 Round 3: 227 peptides, 31 chains. Longest chain 19 peptides. Score 0.526 Round 4: 236 peptides, 32 chains. Longest chain 15 peptides. Score 0.539 Round 5: 228 peptides, 32 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 4 Chains 32, Residues 204, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 7164 restraints for refining 3074 atoms. 6360 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2378 (Rfree = 0.000) for 3074 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 2: After refmac, R = 0.2228 (Rfree = 0.000) for 3031 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2083 (Rfree = 0.000) for 3006 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 4: After refmac, R = 0.2058 (Rfree = 0.000) for 2983 atoms. Found 5 (19 requested) and removed 17 (9 requested) atoms. Cycle 5: After refmac, R = 0.2057 (Rfree = 0.000) for 2958 atoms. Found 15 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 3158 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3176 seeds are put forward Round 1: 194 peptides, 33 chains. Longest chain 13 peptides. Score 0.398 Round 2: 206 peptides, 29 chains. Longest chain 14 peptides. Score 0.491 Round 3: 218 peptides, 30 chains. Longest chain 15 peptides. Score 0.513 Round 4: 221 peptides, 31 chains. Longest chain 20 peptides. Score 0.509 Round 5: 221 peptides, 29 chains. Longest chain 22 peptides. Score 0.535 Taking the results from Round 5 Chains 29, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 6986 restraints for refining 3048 atoms. 6247 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2232 (Rfree = 0.000) for 3048 atoms. Found 10 (19 requested) and removed 22 (9 requested) atoms. Cycle 7: After refmac, R = 0.2122 (Rfree = 0.000) for 3008 atoms. Found 14 (19 requested) and removed 22 (9 requested) atoms. Cycle 8: After refmac, R = 0.1704 (Rfree = 0.000) for 2992 atoms. Found 3 (19 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.1854 (Rfree = 0.000) for 2975 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.1561 (Rfree = 0.000) for 2968 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 3137 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3163 seeds are put forward Round 1: 210 peptides, 37 chains. Longest chain 11 peptides. Score 0.394 Round 2: 235 peptides, 34 chains. Longest chain 18 peptides. Score 0.511 Round 3: 227 peptides, 31 chains. Longest chain 18 peptides. Score 0.526 Round 4: 232 peptides, 27 chains. Longest chain 19 peptides. Score 0.588 Round 5: 242 peptides, 32 chains. Longest chain 14 peptides. Score 0.555 Taking the results from Round 4 Chains 27, Residues 205, Estimated correctness of the model 9.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 6830 restraints for refining 3058 atoms. 6037 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1917 (Rfree = 0.000) for 3058 atoms. Found 10 (19 requested) and removed 27 (9 requested) atoms. Cycle 12: After refmac, R = 0.1862 (Rfree = 0.000) for 3028 atoms. Found 10 (19 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.1852 (Rfree = 0.000) for 3017 atoms. Found 11 (19 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1739 (Rfree = 0.000) for 3005 atoms. Found 6 (19 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.1739 (Rfree = 0.000) for 2986 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 3140 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3154 seeds are put forward Round 1: 203 peptides, 35 chains. Longest chain 14 peptides. Score 0.399 Round 2: 222 peptides, 30 chains. Longest chain 16 peptides. Score 0.525 Round 3: 221 peptides, 31 chains. Longest chain 13 peptides. Score 0.509 Round 4: 209 peptides, 30 chains. Longest chain 16 peptides. Score 0.487 Round 5: 224 peptides, 29 chains. Longest chain 20 peptides. Score 0.543 Taking the results from Round 5 Chains 29, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 6847 restraints for refining 3075 atoms. 6096 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2043 (Rfree = 0.000) for 3075 atoms. Found 16 (19 requested) and removed 20 (9 requested) atoms. Cycle 17: After refmac, R = 0.1883 (Rfree = 0.000) for 3052 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. Cycle 18: After refmac, R = 0.1809 (Rfree = 0.000) for 3041 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.1727 (Rfree = 0.000) for 3031 atoms. Found 4 (19 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1695 (Rfree = 0.000) for 3015 atoms. Found 10 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3220 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 9 peptides. Score 0.299 Round 2: 211 peptides, 34 chains. Longest chain 14 peptides. Score 0.439 Round 3: 206 peptides, 26 chains. Longest chain 21 peptides. Score 0.531 Round 4: 216 peptides, 28 chains. Longest chain 18 peptides. Score 0.533 Round 5: 229 peptides, 28 chains. Longest chain 22 peptides. Score 0.568 Taking the results from Round 5 Chains 28, Residues 201, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 6861 restraints for refining 3075 atoms. 6085 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1920 (Rfree = 0.000) for 3075 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 22: After refmac, R = 0.1762 (Rfree = 0.000) for 3062 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.1730 (Rfree = 0.000) for 3051 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 24: After refmac, R = 0.1695 (Rfree = 0.000) for 3045 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1647 (Rfree = 0.000) for 3038 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3255 seeds are put forward Round 1: 157 peptides, 29 chains. Longest chain 13 peptides. Score 0.330 Round 2: 182 peptides, 30 chains. Longest chain 17 peptides. Score 0.401 Round 3: 197 peptides, 33 chains. Longest chain 16 peptides. Score 0.408 Round 4: 182 peptides, 30 chains. Longest chain 13 peptides. Score 0.401 Round 5: 184 peptides, 29 chains. Longest chain 12 peptides. Score 0.423 Taking the results from Round 5 Chains 29, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 7221 restraints for refining 3075 atoms. 6630 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2103 (Rfree = 0.000) for 3075 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 27: After refmac, R = 0.1848 (Rfree = 0.000) for 3066 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.1738 (Rfree = 0.000) for 3061 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 29: After refmac, R = 0.1732 (Rfree = 0.000) for 3053 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1687 (Rfree = 0.000) for 3047 atoms. Found 10 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 151 peptides, 33 chains. Longest chain 10 peptides. Score 0.243 Round 2: 173 peptides, 32 chains. Longest chain 12 peptides. Score 0.341 Round 3: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.357 Round 4: 170 peptides, 31 chains. Longest chain 13 peptides. Score 0.345 Round 5: 170 peptides, 27 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 5 Chains 27, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 7203 restraints for refining 3074 atoms. 6658 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2164 (Rfree = 0.000) for 3074 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.1980 (Rfree = 0.000) for 3067 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.1911 (Rfree = 0.000) for 3071 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 34: After refmac, R = 0.1934 (Rfree = 0.000) for 3070 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1844 (Rfree = 0.000) for 3075 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3268 seeds are put forward Round 1: 143 peptides, 33 chains. Longest chain 7 peptides. Score 0.212 Round 2: 173 peptides, 34 chains. Longest chain 9 peptides. Score 0.310 Round 3: 176 peptides, 34 chains. Longest chain 8 peptides. Score 0.321 Round 4: 170 peptides, 31 chains. Longest chain 12 peptides. Score 0.345 Round 5: 171 peptides, 32 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 4 Chains 31, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 7291 restraints for refining 3074 atoms. 6766 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1992 (Rfree = 0.000) for 3074 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 37: After refmac, R = 0.1857 (Rfree = 0.000) for 3073 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. Cycle 38: After refmac, R = 0.1828 (Rfree = 0.000) for 3073 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.1836 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.1811 (Rfree = 0.000) for 3070 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 3250 seeds are put forward NCS extension: 0 residues added, 3250 seeds are put forward Round 1: 144 peptides, 32 chains. Longest chain 7 peptides. Score 0.232 Round 2: 169 peptides, 33 chains. Longest chain 11 peptides. Score 0.311 Round 3: 172 peptides, 33 chains. Longest chain 7 peptides. Score 0.322 Round 4: 172 peptides, 30 chains. Longest chain 11 peptides. Score 0.367 Round 5: 166 peptides, 30 chains. Longest chain 8 peptides. Score 0.346 Taking the results from Round 4 Chains 30, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5619 reflections ( 99.79 % complete ) and 7345 restraints for refining 3075 atoms. 6807 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2142 (Rfree = 0.000) for 3075 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 42: After refmac, R = 0.2095 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.2042 (Rfree = 0.000) for 3066 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.1972 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.1936 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.37 Search for helices and strands: 0 residues in 0 chains, 3228 seeds are put forward NCS extension: 0 residues added, 3228 seeds are put forward Round 1: 144 peptides, 32 chains. Longest chain 9 peptides. Score 0.232 Round 2: 160 peptides, 30 chains. Longest chain 11 peptides. Score 0.325 Round 3: 157 peptides, 29 chains. Longest chain 10 peptides. Score 0.330 Round 4: 156 peptides, 27 chains. Longest chain 15 peptides. Score 0.357 Round 5: 160 peptides, 30 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 129, 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 1zkg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5619 reflections ( 99.79 % complete ) and 7358 restraints for refining 3075 atoms. 6869 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1911 (Rfree = 0.000) for 3075 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1921 (Rfree = 0.000) for 3058 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2062 (Rfree = 0.000) for 3045 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1985 (Rfree = 0.000) for 3033 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:05:18 GMT 2018 Job finished. TimeTaking 40.93 Used memory is bytes: 14823136