null Mon 24 Dec 08:02:44 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 1vkh-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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/1vkh-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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 08:02:48 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/1vkh-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6036 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-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: 4 Cell parameters: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.65 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: 19.289 3.600 Wilson plot Bfac: 53.96 5789 reflections ( 99.30 % complete ) and 0 restraints for refining 4822 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3329 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3210 (Rfree = 0.000) for 4822 atoms. Found 30 (30 requested) and removed 57 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 4937 seeds are put forward NCS extension: 0 residues added, 4937 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 9 peptides. Score 0.279 Round 2: 202 peptides, 38 chains. Longest chain 13 peptides. Score 0.348 Round 3: 206 peptides, 39 chains. Longest chain 10 peptides. Score 0.347 Round 4: 217 peptides, 35 chains. Longest chain 11 peptides. Score 0.437 Round 5: 235 peptides, 39 chains. Longest chain 13 peptides. Score 0.439 Taking the results from Round 5 Chains 39, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9380 restraints for refining 3960 atoms. 8635 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2625 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 69 (12 requested) atoms. Cycle 2: After refmac, R = 0.2476 (Rfree = 0.000) for 3877 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 3: After refmac, R = 0.2430 (Rfree = 0.000) for 3867 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 4: After refmac, R = 0.1888 (Rfree = 0.000) for 3856 atoms. Found 12 (24 requested) and removed 20 (12 requested) atoms. Cycle 5: After refmac, R = 0.1761 (Rfree = 0.000) for 3842 atoms. Found 3 (24 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 3982 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3992 seeds are put forward Round 1: 187 peptides, 41 chains. Longest chain 8 peptides. Score 0.252 Round 2: 227 peptides, 44 chains. Longest chain 10 peptides. Score 0.347 Round 3: 235 peptides, 43 chains. Longest chain 12 peptides. Score 0.386 Round 4: 226 peptides, 36 chains. Longest chain 13 peptides. Score 0.451 Round 5: 220 peptides, 37 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 4 Chains 36, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9385 restraints for refining 3960 atoms. 8661 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2194 (Rfree = 0.000) for 3960 atoms. Found 15 (25 requested) and removed 78 (12 requested) atoms. Cycle 7: After refmac, R = 0.2210 (Rfree = 0.000) for 3875 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 8: After refmac, R = 0.2194 (Rfree = 0.000) for 3865 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 9: After refmac, R = 0.1950 (Rfree = 0.000) for 3854 atoms. Found 24 (24 requested) and removed 16 (12 requested) atoms. Cycle 10: After refmac, R = 0.1550 (Rfree = 0.000) for 3859 atoms. Found 10 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 4007 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4026 seeds are put forward Round 1: 206 peptides, 44 chains. Longest chain 7 peptides. Score 0.276 Round 2: 225 peptides, 40 chains. Longest chain 10 peptides. Score 0.395 Round 3: 223 peptides, 36 chains. Longest chain 14 peptides. Score 0.442 Round 4: 240 peptides, 39 chains. Longest chain 12 peptides. Score 0.454 Round 5: 232 peptides, 36 chains. Longest chain 13 peptides. Score 0.469 Taking the results from Round 5 Chains 36, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9389 restraints for refining 3960 atoms. 8641 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1966 (Rfree = 0.000) for 3960 atoms. Found 21 (25 requested) and removed 30 (12 requested) atoms. Cycle 12: After refmac, R = 0.1951 (Rfree = 0.000) for 3930 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 13: After refmac, R = 0.1944 (Rfree = 0.000) for 3923 atoms. Found 24 (25 requested) and removed 22 (12 requested) atoms. Cycle 14: After refmac, R = 0.1871 (Rfree = 0.000) for 3918 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 15: After refmac, R = 0.2001 (Rfree = 0.000) for 3910 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 4076 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4094 seeds are put forward Round 1: 198 peptides, 41 chains. Longest chain 9 peptides. Score 0.291 Round 2: 216 peptides, 42 chains. Longest chain 11 peptides. Score 0.338 Round 3: 233 peptides, 41 chains. Longest chain 11 peptides. Score 0.407 Round 4: 227 peptides, 41 chains. Longest chain 13 peptides. Score 0.388 Round 5: 210 peptides, 32 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 5 Chains 32, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9495 restraints for refining 3960 atoms. 8815 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2051 (Rfree = 0.000) for 3960 atoms. Found 22 (25 requested) and removed 26 (12 requested) atoms. Cycle 17: After refmac, R = 0.2086 (Rfree = 0.000) for 3953 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 18: After refmac, R = 0.2111 (Rfree = 0.000) for 3953 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 19: After refmac, R = 0.1519 (Rfree = 0.000) for 3950 atoms. Found 9 (25 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.1681 (Rfree = 0.000) for 3935 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 4101 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4119 seeds are put forward Round 1: 170 peptides, 36 chains. Longest chain 12 peptides. Score 0.266 Round 2: 212 peptides, 39 chains. Longest chain 13 peptides. Score 0.367 Round 3: 224 peptides, 39 chains. Longest chain 12 peptides. Score 0.405 Round 4: 218 peptides, 39 chains. Longest chain 12 peptides. Score 0.386 Round 5: 212 peptides, 35 chains. Longest chain 13 peptides. Score 0.422 Taking the results from Round 5 Chains 35, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9386 restraints for refining 3959 atoms. 8713 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2111 (Rfree = 0.000) for 3959 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 22: After refmac, R = 0.1916 (Rfree = 0.000) for 3949 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 23: After refmac, R = 0.2022 (Rfree = 0.000) for 3946 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. Cycle 24: After refmac, R = 0.1769 (Rfree = 0.000) for 3934 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 25: After refmac, R = 0.1788 (Rfree = 0.000) for 3938 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 4098 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4115 seeds are put forward Round 1: 190 peptides, 39 chains. Longest chain 9 peptides. Score 0.292 Round 2: 216 peptides, 38 chains. Longest chain 12 peptides. Score 0.394 Round 3: 225 peptides, 39 chains. Longest chain 11 peptides. Score 0.408 Round 4: 228 peptides, 37 chains. Longest chain 13 peptides. Score 0.444 Round 5: 217 peptides, 37 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 4 Chains 37, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9437 restraints for refining 3960 atoms. 8710 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2052 (Rfree = 0.000) for 3960 atoms. Found 23 (25 requested) and removed 22 (12 requested) atoms. Cycle 27: After refmac, R = 0.1984 (Rfree = 0.000) for 3948 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 28: After refmac, R = 0.2016 (Rfree = 0.000) for 3946 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 29: After refmac, R = 0.1914 (Rfree = 0.000) for 3938 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 30: After refmac, R = 0.1600 (Rfree = 0.000) for 3938 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 4058 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4075 seeds are put forward Round 1: 175 peptides, 37 chains. Longest chain 11 peptides. Score 0.269 Round 2: 206 peptides, 38 chains. Longest chain 11 peptides. Score 0.361 Round 3: 213 peptides, 38 chains. Longest chain 11 peptides. Score 0.384 Round 4: 210 peptides, 35 chains. Longest chain 13 peptides. Score 0.415 Round 5: 214 peptides, 37 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 4 Chains 35, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9452 restraints for refining 3960 atoms. 8787 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2077 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 32: After refmac, R = 0.2145 (Rfree = 0.000) for 3950 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.2006 (Rfree = 0.000) for 3955 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 34: After refmac, R = 0.1576 (Rfree = 0.000) for 3956 atoms. Found 8 (25 requested) and removed 15 (12 requested) atoms. Cycle 35: After refmac, R = 0.1442 (Rfree = 0.000) for 3941 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 4053 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4066 seeds are put forward Round 1: 178 peptides, 36 chains. Longest chain 9 peptides. Score 0.294 Round 2: 205 peptides, 36 chains. Longest chain 12 peptides. Score 0.386 Round 3: 201 peptides, 37 chains. Longest chain 13 peptides. Score 0.359 Round 4: 214 peptides, 37 chains. Longest chain 14 peptides. Score 0.401 Round 5: 205 peptides, 36 chains. Longest chain 15 peptides. Score 0.386 Taking the results from Round 4 Chains 37, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9547 restraints for refining 3959 atoms. 8876 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2066 (Rfree = 0.000) for 3959 atoms. Found 21 (25 requested) and removed 20 (12 requested) atoms. Cycle 37: After refmac, R = 0.2118 (Rfree = 0.000) for 3949 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 38: After refmac, R = 0.2133 (Rfree = 0.000) for 3950 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 39: After refmac, R = 0.1983 (Rfree = 0.000) for 3948 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 40: After refmac, R = 0.2011 (Rfree = 0.000) for 3950 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 4108 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4125 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 7 peptides. Score 0.242 Round 2: 169 peptides, 32 chains. Longest chain 10 peptides. Score 0.323 Round 3: 182 peptides, 31 chains. Longest chain 15 peptides. Score 0.381 Round 4: 181 peptides, 31 chains. Longest chain 11 peptides. Score 0.378 Round 5: 190 peptides, 33 chains. Longest chain 11 peptides. Score 0.379 Taking the results from Round 3 Chains 31, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9638 restraints for refining 3960 atoms. 9065 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2109 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 26 (12 requested) atoms. Cycle 42: After refmac, R = 0.2142 (Rfree = 0.000) for 3953 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 43: After refmac, R = 0.2063 (Rfree = 0.000) for 3950 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 44: After refmac, R = 0.1610 (Rfree = 0.000) for 3955 atoms. Found 13 (25 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.1528 (Rfree = 0.000) for 3946 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 4070 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4092 seeds are put forward Round 1: 155 peptides, 35 chains. Longest chain 8 peptides. Score 0.225 Round 2: 176 peptides, 34 chains. Longest chain 15 peptides. Score 0.317 Round 3: 166 peptides, 30 chains. Longest chain 10 peptides. Score 0.342 Round 4: 175 peptides, 31 chains. Longest chain 15 peptides. Score 0.358 Round 5: 171 peptides, 31 chains. Longest chain 10 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 144, 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 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5789 reflections ( 99.30 % complete ) and 9639 restraints for refining 3960 atoms. 9094 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1941 (Rfree = 0.000) for 3960 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2024 (Rfree = 0.000) for 3941 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2066 (Rfree = 0.000) for 3922 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1967 (Rfree = 0.000) for 3908 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:44:18 GMT 2018 Job finished. TimeTaking 41.57 Used memory is bytes: 22170976