Sun 23 Dec 23:53:44 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 2od6-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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/2od6-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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 ============================================================ Sun 23 Dec 23:53:49 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/2od6-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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 304 and 0 Target number of residues in the AU: 304 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.8-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: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3520 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: 29.066 3.800 Wilson plot Bfac: 87.53 5189 reflections ( 98.56 % complete ) and 0 restraints for refining 3908 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3481 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3335 (Rfree = 0.000) for 3908 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 3979 seeds are put forward NCS extension: 0 residues added, 3979 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 9 peptides. Score 0.280 Round 2: 230 peptides, 38 chains. Longest chain 15 peptides. Score 0.443 Round 3: 241 peptides, 40 chains. Longest chain 12 peptides. Score 0.450 Round 4: 251 peptides, 37 chains. Longest chain 19 peptides. Score 0.518 Round 5: 247 peptides, 32 chains. Longest chain 14 peptides. Score 0.567 Taking the results from Round 5 Chains 34, Residues 215, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7117 restraints for refining 3181 atoms. 6208 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2827 (Rfree = 0.000) for 3181 atoms. Found 14 (17 requested) and removed 24 (8 requested) atoms. Cycle 2: After refmac, R = 0.2791 (Rfree = 0.000) for 3121 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2588 (Rfree = 0.000) for 3084 atoms. Found 16 (17 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.2212 (Rfree = 0.000) for 3064 atoms. Found 4 (16 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.2489 (Rfree = 0.000) for 3035 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 3155 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3170 seeds are put forward Round 1: 203 peptides, 39 chains. Longest chain 10 peptides. Score 0.341 Round 2: 230 peptides, 38 chains. Longest chain 14 peptides. Score 0.443 Round 3: 237 peptides, 36 chains. Longest chain 18 peptides. Score 0.490 Round 4: 241 peptides, 41 chains. Longest chain 13 peptides. Score 0.437 Round 5: 262 peptides, 40 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 5 Chains 40, Residues 222, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7302 restraints for refining 3184 atoms. 6454 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2806 (Rfree = 0.000) for 3184 atoms. Found 16 (17 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.2554 (Rfree = 0.000) for 3163 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2662 (Rfree = 0.000) for 3144 atoms. Found 14 (17 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2446 (Rfree = 0.000) for 3125 atoms. Found 8 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2396 (Rfree = 0.000) for 3105 atoms. Found 12 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 3256 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3270 seeds are put forward Round 1: 177 peptides, 34 chains. Longest chain 12 peptides. Score 0.324 Round 2: 207 peptides, 35 chains. Longest chain 16 peptides. Score 0.411 Round 3: 218 peptides, 34 chains. Longest chain 15 peptides. Score 0.460 Round 4: 226 peptides, 35 chains. Longest chain 16 peptides. Score 0.471 Round 5: 228 peptides, 31 chains. Longest chain 15 peptides. Score 0.528 Taking the results from Round 5 Chains 31, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7385 restraints for refining 3184 atoms. 6628 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2646 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2519 (Rfree = 0.000) for 3164 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 13: After refmac, R = 0.2475 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2362 (Rfree = 0.000) for 3137 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2491 (Rfree = 0.000) for 3130 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.60 Search for helices and strands: 0 residues in 0 chains, 3297 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3321 seeds are put forward Round 1: 163 peptides, 36 chains. Longest chain 7 peptides. Score 0.242 Round 2: 205 peptides, 38 chains. Longest chain 8 peptides. Score 0.362 Round 3: 217 peptides, 38 chains. Longest chain 11 peptides. Score 0.402 Round 4: 197 peptides, 31 chains. Longest chain 10 peptides. Score 0.435 Round 5: 195 peptides, 31 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 4 Chains 31, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7473 restraints for refining 3184 atoms. 6840 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2792 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 17: After refmac, R = 0.2585 (Rfree = 0.000) for 3148 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 18: After refmac, R = 0.2660 (Rfree = 0.000) for 3127 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.2536 (Rfree = 0.000) for 3117 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.2541 (Rfree = 0.000) for 3106 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 3246 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3254 seeds are put forward Round 1: 171 peptides, 35 chains. Longest chain 8 peptides. Score 0.287 Round 2: 187 peptides, 34 chains. Longest chain 11 peptides. Score 0.359 Round 3: 207 peptides, 30 chains. Longest chain 17 peptides. Score 0.480 Round 4: 218 peptides, 32 chains. Longest chain 15 peptides. Score 0.486 Round 5: 207 peptides, 32 chains. Longest chain 17 peptides. Score 0.453 Taking the results from Round 4 Chains 32, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5189 reflections ( 98.56 % complete ) and 7033 restraints for refining 3155 atoms. 6321 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2550 (Rfree = 0.000) for 3155 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 22: After refmac, R = 0.2490 (Rfree = 0.000) for 3119 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 23: After refmac, R = 0.2336 (Rfree = 0.000) for 3101 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 24: After refmac, R = 0.2532 (Rfree = 0.000) for 3087 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 25: After refmac, R = 0.2288 (Rfree = 0.000) for 3078 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 3196 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3214 seeds are put forward Round 1: 150 peptides, 33 chains. Longest chain 8 peptides. Score 0.239 Round 2: 187 peptides, 33 chains. Longest chain 14 peptides. Score 0.374 Round 3: 188 peptides, 30 chains. Longest chain 13 peptides. Score 0.420 Round 4: 197 peptides, 33 chains. Longest chain 13 peptides. Score 0.407 Round 5: 193 peptides, 31 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 5 Chains 31, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7471 restraints for refining 3182 atoms. 6854 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2449 (Rfree = 0.000) for 3182 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 27: After refmac, R = 0.2514 (Rfree = 0.000) for 3156 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 28: After refmac, R = 0.2637 (Rfree = 0.000) for 3138 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 29: After refmac, R = 0.2330 (Rfree = 0.000) for 3130 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2239 (Rfree = 0.000) for 3125 atoms. Found 17 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.57 Search for helices and strands: 0 residues in 0 chains, 3255 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3278 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 9 peptides. Score 0.254 Round 2: 174 peptides, 34 chains. Longest chain 12 peptides. Score 0.313 Round 3: 162 peptides, 29 chains. Longest chain 16 peptides. Score 0.347 Round 4: 177 peptides, 32 chains. Longest chain 11 peptides. Score 0.354 Round 5: 171 peptides, 26 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 26, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7547 restraints for refining 3183 atoms. 6993 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2503 (Rfree = 0.000) for 3183 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2655 (Rfree = 0.000) for 3158 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 33: After refmac, R = 0.2500 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.2552 (Rfree = 0.000) for 3129 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 35: After refmac, R = 0.2520 (Rfree = 0.000) for 3121 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3252 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 7 peptides. Score 0.263 Round 2: 144 peptides, 26 chains. Longest chain 12 peptides. Score 0.329 Round 3: 147 peptides, 26 chains. Longest chain 11 peptides. Score 0.340 Round 4: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.368 Round 5: 153 peptides, 25 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 5 Chains 25, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7249 restraints for refining 3099 atoms. 6762 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2776 (Rfree = 0.000) for 3099 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 37: After refmac, R = 0.2673 (Rfree = 0.000) for 3086 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.2607 (Rfree = 0.000) for 3073 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 39: After refmac, R = 0.2534 (Rfree = 0.000) for 3054 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.2548 (Rfree = 0.000) for 3050 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 3130 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3151 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 6 peptides. Score 0.217 Round 2: 135 peptides, 28 chains. Longest chain 7 peptides. Score 0.262 Round 3: 146 peptides, 29 chains. Longest chain 8 peptides. Score 0.288 Round 4: 139 peptides, 26 chains. Longest chain 9 peptides. Score 0.310 Round 5: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.353 Taking the results from Round 5 Chains 22, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 6854 restraints for refining 2986 atoms. 6432 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2659 (Rfree = 0.000) for 2986 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.2602 (Rfree = 0.000) for 2974 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 43: After refmac, R = 0.2334 (Rfree = 0.000) for 2965 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.2409 (Rfree = 0.000) for 2962 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.2355 (Rfree = 0.000) for 2963 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 3053 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3068 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 6 peptides. Score 0.219 Round 2: 144 peptides, 29 chains. Longest chain 7 peptides. Score 0.281 Round 3: 149 peptides, 27 chains. Longest chain 14 peptides. Score 0.331 Round 4: 140 peptides, 26 chains. Longest chain 10 peptides. Score 0.314 Round 5: 147 peptides, 24 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 123, 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 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5189 reflections ( 98.56 % complete ) and 6857 restraints for refining 3023 atoms. 6389 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2572 (Rfree = 0.000) for 3023 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2387 (Rfree = 0.000) for 2996 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2402 (Rfree = 0.000) for 2980 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2365 (Rfree = 0.000) for 2963 atoms. TimeTaking 41.45