Mon 24 Dec 07:37:25 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 2p8j-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-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/2p8j-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-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 07:37:29 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/2p8j-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-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 408 and 0 Target number of residues in the AU: 408 Target solvent content: 0.6584 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.10 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: 72.625 3.802 Wilson plot Bfac: 83.44 6663 reflections ( 98.27 % complete ) and 0 restraints for refining 3705 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3483 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3156 (Rfree = 0.000) for 3705 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 0 residues added, 3784 seeds are put forward Round 1: 242 peptides, 36 chains. Longest chain 17 peptides. Score 0.444 Round 2: 266 peptides, 32 chains. Longest chain 19 peptides. Score 0.539 Round 3: 278 peptides, 33 chains. Longest chain 22 peptides. Score 0.555 Round 4: 251 peptides, 27 chains. Longest chain 22 peptides. Score 0.557 Round 5: 252 peptides, 26 chains. Longest chain 22 peptides. Score 0.569 Taking the results from Round 5 Chains 26, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6935 restraints for refining 3024 atoms. 6057 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2548 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 2: After refmac, R = 0.2356 (Rfree = 0.000) for 2994 atoms. Found 12 (16 requested) and removed 18 (8 requested) atoms. Cycle 3: After refmac, R = 0.2230 (Rfree = 0.000) for 2972 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2189 (Rfree = 0.000) for 2961 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2079 (Rfree = 0.000) for 2954 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3086 seeds are put forward Round 1: 249 peptides, 33 chains. Longest chain 22 peptides. Score 0.492 Round 2: 260 peptides, 33 chains. Longest chain 23 peptides. Score 0.517 Round 3: 266 peptides, 29 chains. Longest chain 23 peptides. Score 0.568 Round 4: 268 peptides, 29 chains. Longest chain 22 peptides. Score 0.572 Round 5: 286 peptides, 30 chains. Longest chain 33 peptides. Score 0.598 Taking the results from Round 5 Chains 31, Residues 256, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6362 restraints for refining 3024 atoms. 5314 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 7: After refmac, R = 0.2304 (Rfree = 0.000) for 3002 atoms. Found 13 (16 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2202 (Rfree = 0.000) for 2999 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2187 (Rfree = 0.000) for 2986 atoms. Found 1 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 2974 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 2.99 Search for helices and strands: 0 residues in 0 chains, 3102 seeds are put forward NCS extension: 39 residues added (5 deleted due to clashes), 3141 seeds are put forward Round 1: 238 peptides, 30 chains. Longest chain 17 peptides. Score 0.498 Round 2: 243 peptides, 28 chains. Longest chain 20 peptides. Score 0.530 Round 3: 265 peptides, 25 chains. Longest chain 25 peptides. Score 0.604 Round 4: 255 peptides, 27 chains. Longest chain 26 peptides. Score 0.565 Round 5: 269 peptides, 29 chains. Longest chain 23 peptides. Score 0.574 Taking the results from Round 3 Chains 27, Residues 240, Estimated correctness of the model 0.6 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6372 restraints for refining 3024 atoms. 5345 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2534 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 12: After refmac, R = 0.2419 (Rfree = 0.000) for 2993 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2243 (Rfree = 0.000) for 2987 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2239 (Rfree = 0.000) for 2984 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.2168 (Rfree = 0.000) for 2971 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 3098 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3114 seeds are put forward Round 1: 242 peptides, 38 chains. Longest chain 12 peptides. Score 0.423 Round 2: 276 peptides, 37 chains. Longest chain 15 peptides. Score 0.512 Round 3: 281 peptides, 32 chains. Longest chain 28 peptides. Score 0.570 Round 4: 262 peptides, 29 chains. Longest chain 20 peptides. Score 0.560 Round 5: 263 peptides, 32 chains. Longest chain 20 peptides. Score 0.533 Taking the results from Round 3 Chains 32, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6454 restraints for refining 3024 atoms. 5490 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2425 (Rfree = 0.000) for 3024 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 2997 atoms. Found 4 (16 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 2983 atoms. Found 8 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2234 (Rfree = 0.000) for 2975 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2195 (Rfree = 0.000) for 2971 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 2.98 Search for helices and strands: 0 residues in 0 chains, 3099 seeds are put forward NCS extension: 45 residues added (2 deleted due to clashes), 3144 seeds are put forward Round 1: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.411 Round 2: 254 peptides, 32 chains. Longest chain 20 peptides. Score 0.514 Round 3: 271 peptides, 36 chains. Longest chain 20 peptides. Score 0.511 Round 4: 264 peptides, 29 chains. Longest chain 21 peptides. Score 0.564 Round 5: 272 peptides, 31 chains. Longest chain 34 peptides. Score 0.561 Taking the results from Round 4 Chains 29, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6639 restraints for refining 3023 atoms. 5728 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2546 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2305 (Rfree = 0.000) for 3002 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.2266 (Rfree = 0.000) for 2995 atoms. Found 4 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.2279 (Rfree = 0.000) for 2980 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.2264 (Rfree = 0.000) for 2975 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 2.98 Search for helices and strands: 0 residues in 0 chains, 3067 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3082 seeds are put forward Round 1: 234 peptides, 34 chains. Longest chain 16 peptides. Score 0.446 Round 2: 255 peptides, 34 chains. Longest chain 19 peptides. Score 0.495 Round 3: 251 peptides, 30 chains. Longest chain 19 peptides. Score 0.527 Round 4: 240 peptides, 31 chains. Longest chain 27 peptides. Score 0.492 Round 5: 247 peptides, 27 chains. Longest chain 20 peptides. Score 0.549 Taking the results from Round 5 Chains 27, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6681 restraints for refining 3023 atoms. 5828 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2571 (Rfree = 0.000) for 3023 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 27: After refmac, R = 0.2225 (Rfree = 0.000) for 3007 atoms. Found 13 (16 requested) and removed 10 (8 requested) atoms. Cycle 28: After refmac, R = 0.2120 (Rfree = 0.000) for 3003 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Cycle 29: After refmac, R = 0.2062 (Rfree = 0.000) for 2996 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1913 (Rfree = 0.000) for 2995 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 3077 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3106 seeds are put forward Round 1: 233 peptides, 34 chains. Longest chain 17 peptides. Score 0.444 Round 2: 247 peptides, 35 chains. Longest chain 19 peptides. Score 0.467 Round 3: 250 peptides, 31 chains. Longest chain 22 peptides. Score 0.515 Round 4: 244 peptides, 29 chains. Longest chain 24 peptides. Score 0.522 Round 5: 246 peptides, 30 chains. Longest chain 26 peptides. Score 0.516 Taking the results from Round 4 Chains 29, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6655 restraints for refining 3024 atoms. 5824 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2552 (Rfree = 0.000) for 3024 atoms. Found 13 (16 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2202 (Rfree = 0.000) for 3005 atoms. Found 12 (16 requested) and removed 17 (8 requested) atoms. Cycle 33: After refmac, R = 0.2134 (Rfree = 0.000) for 2989 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.2115 (Rfree = 0.000) for 2976 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2095 (Rfree = 0.000) for 2968 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 3061 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 3102 seeds are put forward Round 1: 209 peptides, 32 chains. Longest chain 15 peptides. Score 0.407 Round 2: 241 peptides, 35 chains. Longest chain 18 peptides. Score 0.452 Round 3: 240 peptides, 34 chains. Longest chain 14 peptides. Score 0.461 Round 4: 257 peptides, 27 chains. Longest chain 20 peptides. Score 0.569 Round 5: 257 peptides, 30 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 4 Chains 27, Residues 230, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6414 restraints for refining 3024 atoms. 5505 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2515 (Rfree = 0.000) for 3024 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.2241 (Rfree = 0.000) for 3011 atoms. Found 14 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2288 (Rfree = 0.000) for 3005 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2186 (Rfree = 0.000) for 2996 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 2993 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3110 seeds are put forward Round 1: 191 peptides, 33 chains. Longest chain 11 peptides. Score 0.347 Round 2: 226 peptides, 33 chains. Longest chain 18 peptides. Score 0.438 Round 3: 237 peptides, 32 chains. Longest chain 18 peptides. Score 0.475 Round 4: 240 peptides, 30 chains. Longest chain 21 peptides. Score 0.503 Round 5: 245 peptides, 30 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 5 Chains 32, Residues 215, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6663 reflections ( 98.27 % complete ) and 6361 restraints for refining 3024 atoms. 5427 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2505 (Rfree = 0.000) for 3024 atoms. Found 15 (16 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.2460 (Rfree = 0.000) for 3000 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.2370 (Rfree = 0.000) for 2985 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 44: After refmac, R = 0.2259 (Rfree = 0.000) for 2977 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.2236 (Rfree = 0.000) for 2968 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.01 Search for helices and strands: 0 residues in 0 chains, 3064 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3086 seeds are put forward Round 1: 197 peptides, 34 chains. Longest chain 11 peptides. Score 0.352 Round 2: 217 peptides, 30 chains. Longest chain 18 peptides. Score 0.449 Round 3: 212 peptides, 31 chains. Longest chain 14 peptides. Score 0.426 Round 4: 214 peptides, 30 chains. Longest chain 18 peptides. Score 0.442 Round 5: 205 peptides, 26 chains. Longest chain 17 peptides. Score 0.465 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 179, 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 2p8j-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6663 reflections ( 98.27 % complete ) and 6893 restraints for refining 3024 atoms. 6203 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2635 (Rfree = 0.000) for 3024 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2431 (Rfree = 0.000) for 3004 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2351 (Rfree = 0.000) for 2984 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2206 (Rfree = 0.000) for 2970 atoms. TimeTaking 41.85