null Mon 24 Dec 00:12:32 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.2-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 00:12:36 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.2-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 325 and 0 Target number of residues in the AU: 325 Target solvent content: 0.6389 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 71.17 7991 reflections ( 99.85 % complete ) and 0 restraints for refining 3770 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3313 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2884 (Rfree = 0.000) for 3770 atoms. Found 33 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 3909 seeds are put forward NCS extension: 0 residues added, 3909 seeds are put forward Round 1: 178 peptides, 36 chains. Longest chain 15 peptides. Score 0.298 Round 2: 227 peptides, 37 chains. Longest chain 14 peptides. Score 0.448 Round 3: 241 peptides, 33 chains. Longest chain 15 peptides. Score 0.540 Round 4: 258 peptides, 35 chains. Longest chain 21 peptides. Score 0.562 Round 5: 239 peptides, 34 chains. Longest chain 20 peptides. Score 0.522 Taking the results from Round 4 Chains 35, Residues 223, Estimated correctness of the model 30.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 7021 restraints for refining 3092 atoms. 6164 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2501 (Rfree = 0.000) for 3092 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 3043 atoms. Found 16 (27 requested) and removed 15 (13 requested) atoms. Cycle 3: After refmac, R = 0.2284 (Rfree = 0.000) for 3019 atoms. Found 17 (27 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2153 (Rfree = 0.000) for 3011 atoms. Found 12 (27 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2110 (Rfree = 0.000) for 3004 atoms. Found 9 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 3180 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3211 seeds are put forward Round 1: 238 peptides, 38 chains. Longest chain 13 peptides. Score 0.468 Round 2: 257 peptides, 33 chains. Longest chain 19 peptides. Score 0.582 Round 3: 256 peptides, 30 chains. Longest chain 16 peptides. Score 0.613 Round 4: 263 peptides, 29 chains. Longest chain 25 peptides. Score 0.640 Round 5: 275 peptides, 28 chains. Longest chain 25 peptides. Score 0.677 Taking the results from Round 5 Chains 29, Residues 247, Estimated correctness of the model 60.1 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6310 restraints for refining 3096 atoms. 5191 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2495 (Rfree = 0.000) for 3096 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 7: After refmac, R = 0.2247 (Rfree = 0.000) for 3083 atoms. Found 17 (27 requested) and removed 18 (13 requested) atoms. Cycle 8: After refmac, R = 0.2184 (Rfree = 0.000) for 3069 atoms. Found 18 (27 requested) and removed 20 (13 requested) atoms. Cycle 9: After refmac, R = 0.2603 (Rfree = 0.000) for 3053 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2659 (Rfree = 0.000) for 3037 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 3201 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3223 seeds are put forward Round 1: 218 peptides, 34 chains. Longest chain 14 peptides. Score 0.461 Round 2: 251 peptides, 30 chains. Longest chain 27 peptides. Score 0.601 Round 3: 248 peptides, 31 chains. Longest chain 29 peptides. Score 0.582 Round 4: 245 peptides, 29 chains. Longest chain 28 peptides. Score 0.598 Round 5: 249 peptides, 32 chains. Longest chain 22 peptides. Score 0.573 Taking the results from Round 2 Chains 30, Residues 221, Estimated correctness of the model 41.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6749 restraints for refining 3070 atoms. 5859 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2212 (Rfree = 0.000) for 3070 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 12: After refmac, R = 0.2083 (Rfree = 0.000) for 3073 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 13: After refmac, R = 0.2075 (Rfree = 0.000) for 3063 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 14: After refmac, R = 0.1901 (Rfree = 0.000) for 3065 atoms. Found 1 (27 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.2299 (Rfree = 0.000) for 3048 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3258 seeds are put forward Round 1: 223 peptides, 35 chains. Longest chain 16 peptides. Score 0.463 Round 2: 246 peptides, 34 chains. Longest chain 20 peptides. Score 0.542 Round 3: 255 peptides, 35 chains. Longest chain 21 peptides. Score 0.554 Round 4: 244 peptides, 36 chains. Longest chain 17 peptides. Score 0.512 Round 5: 248 peptides, 33 chains. Longest chain 20 peptides. Score 0.559 Taking the results from Round 5 Chains 33, Residues 215, Estimated correctness of the model 29.5 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6750 restraints for refining 3096 atoms. 5913 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2243 (Rfree = 0.000) for 3096 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 17: After refmac, R = 0.2137 (Rfree = 0.000) for 3096 atoms. Found 18 (27 requested) and removed 16 (13 requested) atoms. Cycle 18: After refmac, R = 0.2109 (Rfree = 0.000) for 3091 atoms. Found 26 (27 requested) and removed 17 (13 requested) atoms. Cycle 19: After refmac, R = 0.2052 (Rfree = 0.000) for 3094 atoms. Found 15 (27 requested) and removed 17 (13 requested) atoms. Cycle 20: After refmac, R = 0.1992 (Rfree = 0.000) for 3082 atoms. Found 12 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 3256 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 3293 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 14 peptides. Score 0.418 Round 2: 246 peptides, 34 chains. Longest chain 24 peptides. Score 0.542 Round 3: 247 peptides, 35 chains. Longest chain 18 peptides. Score 0.532 Round 4: 240 peptides, 32 chains. Longest chain 17 peptides. Score 0.550 Round 5: 242 peptides, 34 chains. Longest chain 18 peptides. Score 0.531 Taking the results from Round 4 Chains 32, Residues 208, Estimated correctness of the model 26.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6945 restraints for refining 3094 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2229 (Rfree = 0.000) for 3094 atoms. Found 17 (27 requested) and removed 15 (13 requested) atoms. Cycle 22: After refmac, R = 0.2075 (Rfree = 0.000) for 3089 atoms. Found 9 (27 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2004 (Rfree = 0.000) for 3074 atoms. Found 14 (27 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.2056 (Rfree = 0.000) for 3072 atoms. Found 21 (27 requested) and removed 16 (13 requested) atoms. Cycle 25: After refmac, R = 0.2418 (Rfree = 0.000) for 3069 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.06 Search for helices and strands: 0 residues in 0 chains, 3250 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3266 seeds are put forward Round 1: 216 peptides, 34 chains. Longest chain 17 peptides. Score 0.455 Round 2: 244 peptides, 34 chains. Longest chain 17 peptides. Score 0.536 Round 3: 246 peptides, 33 chains. Longest chain 22 peptides. Score 0.554 Round 4: 246 peptides, 38 chains. Longest chain 19 peptides. Score 0.492 Round 5: 241 peptides, 35 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 3 Chains 35, Residues 213, Estimated correctness of the model 28.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6646 restraints for refining 3096 atoms. 5804 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2214 (Rfree = 0.000) for 3096 atoms. Found 22 (27 requested) and removed 27 (13 requested) atoms. Cycle 27: After refmac, R = 0.2044 (Rfree = 0.000) for 3086 atoms. Found 16 (27 requested) and removed 18 (13 requested) atoms. Cycle 28: After refmac, R = 0.1818 (Rfree = 0.000) for 3077 atoms. Found 9 (27 requested) and removed 14 (13 requested) atoms. Cycle 29: After refmac, R = 0.1911 (Rfree = 0.000) for 3069 atoms. Found 14 (27 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.1731 (Rfree = 0.000) for 3067 atoms. Found 3 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 3205 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 3226 seeds are put forward Round 1: 217 peptides, 38 chains. Longest chain 13 peptides. Score 0.403 Round 2: 241 peptides, 34 chains. Longest chain 21 peptides. Score 0.528 Round 3: 231 peptides, 36 chains. Longest chain 17 peptides. Score 0.474 Round 4: 238 peptides, 35 chains. Longest chain 23 peptides. Score 0.507 Round 5: 236 peptides, 35 chains. Longest chain 31 peptides. Score 0.501 Taking the results from Round 2 Chains 35, Residues 207, Estimated correctness of the model 20.2 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6610 restraints for refining 3096 atoms. 5756 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2041 (Rfree = 0.000) for 3096 atoms. Found 24 (27 requested) and removed 15 (13 requested) atoms. Cycle 32: After refmac, R = 0.1891 (Rfree = 0.000) for 3102 atoms. Found 9 (27 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.1807 (Rfree = 0.000) for 3093 atoms. Found 12 (27 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.1891 (Rfree = 0.000) for 3092 atoms. Found 6 (27 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.1852 (Rfree = 0.000) for 3082 atoms. Found 15 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3230 seeds are put forward Round 1: 213 peptides, 43 chains. Longest chain 13 peptides. Score 0.318 Round 2: 233 peptides, 34 chains. Longest chain 20 peptides. Score 0.505 Round 3: 219 peptides, 33 chains. Longest chain 18 peptides. Score 0.477 Round 4: 226 peptides, 36 chains. Longest chain 19 peptides. Score 0.458 Round 5: 229 peptides, 32 chains. Longest chain 21 peptides. Score 0.519 Taking the results from Round 5 Chains 33, Residues 197, Estimated correctness of the model 17.4 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6604 restraints for refining 3096 atoms. 5765 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2228 (Rfree = 0.000) for 3096 atoms. Found 25 (27 requested) and removed 18 (13 requested) atoms. Cycle 37: After refmac, R = 0.1987 (Rfree = 0.000) for 3100 atoms. Found 9 (27 requested) and removed 16 (13 requested) atoms. Cycle 38: After refmac, R = 0.1936 (Rfree = 0.000) for 3086 atoms. Found 10 (27 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1941 (Rfree = 0.000) for 3077 atoms. Found 11 (27 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1807 (Rfree = 0.000) for 3073 atoms. Found 7 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 3207 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 3239 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 13 peptides. Score 0.346 Round 2: 197 peptides, 30 chains. Longest chain 16 peptides. Score 0.450 Round 3: 212 peptides, 32 chains. Longest chain 17 peptides. Score 0.469 Round 4: 217 peptides, 31 chains. Longest chain 17 peptides. Score 0.497 Round 5: 222 peptides, 34 chains. Longest chain 22 peptides. Score 0.473 Taking the results from Round 4 Chains 31, Residues 186, Estimated correctness of the model 10.4 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6856 restraints for refining 3095 atoms. 6128 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2160 (Rfree = 0.000) for 3095 atoms. Found 25 (27 requested) and removed 16 (13 requested) atoms. Cycle 42: After refmac, R = 0.2089 (Rfree = 0.000) for 3101 atoms. Found 11 (27 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.1994 (Rfree = 0.000) for 3094 atoms. Found 12 (27 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.2640 (Rfree = 0.000) for 3083 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 45: After refmac, R = 0.2196 (Rfree = 0.000) for 3080 atoms. Found 18 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 3239 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3267 seeds are put forward Round 1: 178 peptides, 35 chains. Longest chain 16 peptides. Score 0.313 Round 2: 193 peptides, 33 chains. Longest chain 13 peptides. Score 0.395 Round 3: 194 peptides, 29 chains. Longest chain 16 peptides. Score 0.455 Round 4: 209 peptides, 29 chains. Longest chain 17 peptides. Score 0.500 Round 5: 206 peptides, 30 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 180, Estimated correctness of the model 11.3 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1zkg-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (180 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.85 % complete ) and 6788 restraints for refining 3096 atoms. 6084 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2133 (Rfree = 0.000) for 3096 atoms. Found 0 (27 requested) and removed 12 (13 requested) atoms. Cycle 47: After refmac, R = 0.2085 (Rfree = 0.000) for 3079 atoms. Found 0 (27 requested) and removed 4 (13 requested) atoms. Cycle 48: After refmac, R = 0.1944 (Rfree = 0.000) for 3071 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2194 (Rfree = 0.000) for 3054 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:47:30 GMT 2018 Job finished. TimeTaking 34.97 Used memory is bytes: 2191912