Mon 24 Dec 07:42:34 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 2gb5-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2gb5-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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/2gb5-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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 07:42:38 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/2gb5-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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 381 and 0 Target number of residues in the AU: 381 Target solvent content: 0.6498 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-3.8-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.80 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: 49.644 3.800 Wilson plot Bfac: 77.61 6155 reflections ( 99.32 % complete ) and 0 restraints for refining 4774 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3416 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3373 (Rfree = 0.000) for 4774 atoms. Found 15 (26 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 4828 seeds are put forward NCS extension: 0 residues added, 4828 seeds are put forward Round 1: 144 peptides, 33 chains. Longest chain 7 peptides. Score 0.210 Round 2: 191 peptides, 35 chains. Longest chain 14 peptides. Score 0.334 Round 3: 225 peptides, 39 chains. Longest chain 11 peptides. Score 0.382 Round 4: 234 peptides, 36 chains. Longest chain 18 peptides. Score 0.442 Round 5: 232 peptides, 37 chains. Longest chain 18 peptides. Score 0.425 Taking the results from Round 4 Chains 36, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 9249 restraints for refining 3891 atoms. 8493 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3262 (Rfree = 0.000) for 3891 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 2: After refmac, R = 0.3137 (Rfree = 0.000) for 3818 atoms. Found 11 (21 requested) and removed 32 (10 requested) atoms. Cycle 3: After refmac, R = 0.3055 (Rfree = 0.000) for 3750 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 4: After refmac, R = 0.2959 (Rfree = 0.000) for 3713 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. Cycle 5: After refmac, R = 0.2918 (Rfree = 0.000) for 3664 atoms. Found 12 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3801 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 12 peptides. Score 0.260 Round 2: 207 peptides, 37 chains. Longest chain 11 peptides. Score 0.356 Round 3: 225 peptides, 40 chains. Longest chain 13 peptides. Score 0.370 Round 4: 234 peptides, 39 chains. Longest chain 19 peptides. Score 0.407 Round 5: 239 peptides, 41 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 4 Chains 39, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8083 restraints for refining 3505 atoms. 7342 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2941 (Rfree = 0.000) for 3505 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 7: After refmac, R = 0.2865 (Rfree = 0.000) for 3450 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 8: After refmac, R = 0.2535 (Rfree = 0.000) for 3425 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 9: After refmac, R = 0.2522 (Rfree = 0.000) for 3405 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 10: After refmac, R = 0.2466 (Rfree = 0.000) for 3396 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 3485 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3513 seeds are put forward Round 1: 207 peptides, 41 chains. Longest chain 13 peptides. Score 0.305 Round 2: 239 peptides, 43 chains. Longest chain 15 peptides. Score 0.373 Round 3: 247 peptides, 43 chains. Longest chain 11 peptides. Score 0.395 Round 4: 245 peptides, 38 chains. Longest chain 17 peptides. Score 0.448 Round 5: 251 peptides, 37 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Chains 37, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8406 restraints for refining 3701 atoms. 7587 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2824 (Rfree = 0.000) for 3701 atoms. Found 20 (20 requested) and removed 60 (10 requested) atoms. Cycle 12: After refmac, R = 0.2552 (Rfree = 0.000) for 3624 atoms. Found 16 (20 requested) and removed 37 (10 requested) atoms. Cycle 13: After refmac, R = 0.2279 (Rfree = 0.000) for 3583 atoms. Found 10 (19 requested) and removed 47 (9 requested) atoms. Cycle 14: After refmac, R = 0.2125 (Rfree = 0.000) for 3536 atoms. Found 10 (19 requested) and removed 24 (9 requested) atoms. Cycle 15: After refmac, R = 0.2141 (Rfree = 0.000) for 3516 atoms. Found 13 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3613 seeds are put forward Round 1: 219 peptides, 42 chains. Longest chain 16 peptides. Score 0.328 Round 2: 234 peptides, 38 chains. Longest chain 12 peptides. Score 0.419 Round 3: 231 peptides, 38 chains. Longest chain 15 peptides. Score 0.411 Round 4: 216 peptides, 35 chains. Longest chain 17 peptides. Score 0.406 Round 5: 207 peptides, 32 chains. Longest chain 18 peptides. Score 0.417 Taking the results from Round 2 Chains 38, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8268 restraints for refining 3682 atoms. 7522 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2364 (Rfree = 0.000) for 3682 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 17: After refmac, R = 0.2122 (Rfree = 0.000) for 3647 atoms. Found 12 (20 requested) and removed 21 (10 requested) atoms. Cycle 18: After refmac, R = 0.2239 (Rfree = 0.000) for 3618 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 19: After refmac, R = 0.2124 (Rfree = 0.000) for 3596 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 20: After refmac, R = 0.2153 (Rfree = 0.000) for 3584 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3686 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3703 seeds are put forward Round 1: 194 peptides, 38 chains. Longest chain 11 peptides. Score 0.304 Round 2: 211 peptides, 38 chains. Longest chain 13 peptides. Score 0.355 Round 3: 219 peptides, 37 chains. Longest chain 15 peptides. Score 0.390 Round 4: 206 peptides, 31 chains. Longest chain 14 peptides. Score 0.427 Round 5: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 4 Chains 31, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8690 restraints for refining 3788 atoms. 8021 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2337 (Rfree = 0.000) for 3788 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 22: After refmac, R = 0.2139 (Rfree = 0.000) for 3757 atoms. Found 13 (20 requested) and removed 25 (10 requested) atoms. Cycle 23: After refmac, R = 0.2131 (Rfree = 0.000) for 3733 atoms. Found 15 (20 requested) and removed 18 (10 requested) atoms. Cycle 24: After refmac, R = 0.2095 (Rfree = 0.000) for 3706 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 25: After refmac, R = 0.2100 (Rfree = 0.000) for 3696 atoms. Found 19 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 3770 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3789 seeds are put forward Round 1: 181 peptides, 39 chains. Longest chain 9 peptides. Score 0.250 Round 2: 225 peptides, 39 chains. Longest chain 14 peptides. Score 0.382 Round 3: 233 peptides, 38 chains. Longest chain 15 peptides. Score 0.416 Round 4: 224 peptides, 41 chains. Longest chain 12 peptides. Score 0.355 Round 5: 209 peptides, 37 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 3 Chains 38, Residues 195, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8313 restraints for refining 3767 atoms. 7533 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2202 (Rfree = 0.000) for 3767 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 27: After refmac, R = 0.2149 (Rfree = 0.000) for 3730 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 28: After refmac, R = 0.2260 (Rfree = 0.000) for 3725 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2113 (Rfree = 0.000) for 3722 atoms. Found 19 (20 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.1835 (Rfree = 0.000) for 3717 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 3793 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3814 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 11 peptides. Score 0.259 Round 2: 213 peptides, 41 chains. Longest chain 11 peptides. Score 0.323 Round 3: 212 peptides, 38 chains. Longest chain 10 peptides. Score 0.357 Round 4: 224 peptides, 38 chains. Longest chain 14 peptides. Score 0.392 Round 5: 221 peptides, 35 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 35, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6155 reflections ( 99.32 % complete ) and 8909 restraints for refining 3893 atoms. 8200 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2402 (Rfree = 0.000) for 3893 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. Cycle 32: After refmac, R = 0.2318 (Rfree = 0.000) for 3847 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 33: After refmac, R = 0.2166 (Rfree = 0.000) for 3825 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 34: After refmac, R = 0.2172 (Rfree = 0.000) for 3807 atoms. Found 21 (21 requested) and removed 41 (10 requested) atoms. Cycle 35: After refmac, R = 0.1764 (Rfree = 0.000) for 3776 atoms. Found 10 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 3875 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3898 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 9 peptides. Score 0.265 Round 2: 177 peptides, 34 chains. Longest chain 9 peptides. Score 0.304 Round 3: 182 peptides, 33 chains. Longest chain 10 peptides. Score 0.333 Round 4: 185 peptides, 32 chains. Longest chain 11 peptides. Score 0.355 Round 5: 187 peptides, 34 chains. Longest chain 9 peptides. Score 0.335 Taking the results from Round 4 Chains 32, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8927 restraints for refining 3827 atoms. 8347 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2260 (Rfree = 0.000) for 3827 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 37: After refmac, R = 0.2147 (Rfree = 0.000) for 3813 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 38: After refmac, R = 0.2093 (Rfree = 0.000) for 3807 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 39: After refmac, R = 0.2086 (Rfree = 0.000) for 3800 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1734 (Rfree = 0.000) for 3799 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 3875 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 3881 seeds are put forward Round 1: 153 peptides, 32 chains. Longest chain 9 peptides. Score 0.255 Round 2: 179 peptides, 34 chains. Longest chain 9 peptides. Score 0.310 Round 3: 187 peptides, 36 chains. Longest chain 11 peptides. Score 0.309 Round 4: 181 peptides, 31 chains. Longest chain 16 peptides. Score 0.356 Round 5: 179 peptides, 31 chains. Longest chain 12 peptides. Score 0.350 Taking the results from Round 4 Chains 33, Residues 150, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8903 restraints for refining 3893 atoms. 8257 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2107 (Rfree = 0.000) for 3893 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.2213 (Rfree = 0.000) for 3868 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 43: After refmac, R = 0.2283 (Rfree = 0.000) for 3845 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 44: After refmac, R = 0.2284 (Rfree = 0.000) for 3823 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 45: After refmac, R = 0.1806 (Rfree = 0.000) for 3821 atoms. Found 10 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3888 seeds are put forward Round 1: 135 peptides, 29 chains. Longest chain 11 peptides. Score 0.236 Round 2: 159 peptides, 32 chains. Longest chain 12 peptides. Score 0.274 Round 3: 163 peptides, 30 chains. Longest chain 12 peptides. Score 0.314 Round 4: 160 peptides, 29 chains. Longest chain 13 peptides. Score 0.319 Round 5: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, 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 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6155 reflections ( 99.32 % complete ) and 8980 restraints for refining 3801 atoms. 8492 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2398 (Rfree = 0.000) for 3801 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2341 (Rfree = 0.000) for 3777 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2398 (Rfree = 0.000) for 3765 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2258 (Rfree = 0.000) for 3745 atoms. TimeTaking 41.43