Mon 24 Dec 00:54:11 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 2p8j-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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/2p8j-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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 00:54:15 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/2p8j-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-4.0-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 398 and 0 Target number of residues in the AU: 398 Target solvent content: 0.6668 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-4.0-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-4.0-parrot-mrncs.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 4.000 Wilson plot Bfac: 89.83 5718 reflections ( 98.03 % complete ) and 0 restraints for refining 3720 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3468 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3177 (Rfree = 0.000) for 3720 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3807 seeds are put forward NCS extension: 0 residues added, 3807 seeds are put forward Round 1: 202 peptides, 34 chains. Longest chain 13 peptides. Score 0.365 Round 2: 249 peptides, 34 chains. Longest chain 22 peptides. Score 0.482 Round 3: 263 peptides, 34 chains. Longest chain 28 peptides. Score 0.513 Round 4: 278 peptides, 33 chains. Longest chain 29 peptides. Score 0.555 Round 5: 261 peptides, 28 chains. Longest chain 26 peptides. Score 0.568 Taking the results from Round 5 Chains 28, Residues 233, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6657 restraints for refining 3017 atoms. 5723 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2672 (Rfree = 0.000) for 3017 atoms. Found 7 (14 requested) and removed 22 (7 requested) atoms. Cycle 2: After refmac, R = 0.2420 (Rfree = 0.000) for 2948 atoms. Found 12 (14 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2349 (Rfree = 0.000) for 2932 atoms. Found 11 (13 requested) and removed 16 (6 requested) atoms. Cycle 4: After refmac, R = 0.2288 (Rfree = 0.000) for 2913 atoms. Found 6 (13 requested) and removed 16 (6 requested) atoms. Cycle 5: After refmac, R = 0.2286 (Rfree = 0.000) for 2896 atoms. Found 8 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 3005 seeds are put forward NCS extension: 48 residues added (4 deleted due to clashes), 3053 seeds are put forward Round 1: 234 peptides, 32 chains. Longest chain 17 peptides. Score 0.468 Round 2: 251 peptides, 32 chains. Longest chain 15 peptides. Score 0.507 Round 3: 272 peptides, 32 chains. Longest chain 25 peptides. Score 0.552 Round 4: 259 peptides, 29 chains. Longest chain 24 peptides. Score 0.554 Round 5: 264 peptides, 28 chains. Longest chain 26 peptides. Score 0.574 Taking the results from Round 5 Chains 29, Residues 236, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6614 restraints for refining 3020 atoms. 5664 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2566 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 7: After refmac, R = 0.2412 (Rfree = 0.000) for 3006 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2339 (Rfree = 0.000) for 2997 atoms. Found 4 (14 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2342 (Rfree = 0.000) for 2984 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2420 (Rfree = 0.000) for 2976 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.12 Search for helices and strands: 0 residues in 0 chains, 3067 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 3103 seeds are put forward Round 1: 239 peptides, 34 chains. Longest chain 17 peptides. Score 0.458 Round 2: 248 peptides, 24 chains. Longest chain 24 peptides. Score 0.580 Round 3: 242 peptides, 28 chains. Longest chain 24 peptides. Score 0.528 Round 4: 257 peptides, 28 chains. Longest chain 26 peptides. Score 0.560 Round 5: 248 peptides, 26 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 2 Chains 25, Residues 224, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6489 restraints for refining 3020 atoms. 5567 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2572 (Rfree = 0.000) for 3020 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 12: After refmac, R = 0.2290 (Rfree = 0.000) for 3000 atoms. Found 3 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2265 (Rfree = 0.000) for 2979 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.2181 (Rfree = 0.000) for 2961 atoms. Found 3 (14 requested) and removed 12 (7 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 2950 atoms. Found 4 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3084 seeds are put forward Round 1: 224 peptides, 31 chains. Longest chain 19 peptides. Score 0.455 Round 2: 259 peptides, 27 chains. Longest chain 24 peptides. Score 0.573 Round 3: 257 peptides, 29 chains. Longest chain 24 peptides. Score 0.550 Round 4: 253 peptides, 24 chains. Longest chain 24 peptides. Score 0.590 Round 5: 244 peptides, 30 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 4 Chains 24, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6806 restraints for refining 3020 atoms. 5914 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2685 (Rfree = 0.000) for 3020 atoms. Found 13 (14 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.2415 (Rfree = 0.000) for 2986 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.2404 (Rfree = 0.000) for 2979 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2489 (Rfree = 0.000) for 2969 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 20: After refmac, R = 0.2329 (Rfree = 0.000) for 2958 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.10 Search for helices and strands: 0 residues in 0 chains, 3089 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3106 seeds are put forward Round 1: 197 peptides, 29 chains. Longest chain 13 peptides. Score 0.411 Round 2: 253 peptides, 33 chains. Longest chain 15 peptides. Score 0.501 Round 3: 247 peptides, 31 chains. Longest chain 20 peptides. Score 0.508 Round 4: 241 peptides, 27 chains. Longest chain 17 peptides. Score 0.536 Round 5: 247 peptides, 29 chains. Longest chain 20 peptides. Score 0.529 Taking the results from Round 4 Chains 27, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6966 restraints for refining 3019 atoms. 6137 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2421 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2250 (Rfree = 0.000) for 3009 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 23: After refmac, R = 0.2375 (Rfree = 0.000) for 2994 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2385 (Rfree = 0.000) for 2995 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2223 (Rfree = 0.000) for 2987 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3108 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3127 seeds are put forward Round 1: 209 peptides, 35 chains. Longest chain 12 peptides. Score 0.372 Round 2: 245 peptides, 34 chains. Longest chain 17 peptides. Score 0.473 Round 3: 243 peptides, 38 chains. Longest chain 14 peptides. Score 0.425 Round 4: 236 peptides, 33 chains. Longest chain 22 peptides. Score 0.462 Round 5: 262 peptides, 32 chains. Longest chain 20 peptides. Score 0.531 Taking the results from Round 5 Chains 32, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6763 restraints for refining 3019 atoms. 5875 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2377 (Rfree = 0.000) for 3019 atoms. Found 9 (14 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.2324 (Rfree = 0.000) for 2992 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 28: After refmac, R = 0.2448 (Rfree = 0.000) for 2976 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.2354 (Rfree = 0.000) for 2968 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.2252 (Rfree = 0.000) for 2948 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 3101 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3119 seeds are put forward Round 1: 188 peptides, 31 chains. Longest chain 12 peptides. Score 0.363 Round 2: 204 peptides, 31 chains. Longest chain 13 peptides. Score 0.405 Round 3: 219 peptides, 31 chains. Longest chain 15 peptides. Score 0.443 Round 4: 225 peptides, 29 chains. Longest chain 18 peptides. Score 0.479 Round 5: 220 peptides, 31 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 4 Chains 29, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6994 restraints for refining 3020 atoms. 6239 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2820 (Rfree = 0.000) for 3020 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.2504 (Rfree = 0.000) for 2989 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 33: After refmac, R = 0.2427 (Rfree = 0.000) for 2969 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.2428 (Rfree = 0.000) for 2956 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 35: After refmac, R = 0.2252 (Rfree = 0.000) for 2943 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.10 Search for helices and strands: 0 residues in 0 chains, 3059 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3084 seeds are put forward Round 1: 204 peptides, 34 chains. Longest chain 18 peptides. Score 0.371 Round 2: 235 peptides, 35 chains. Longest chain 19 peptides. Score 0.438 Round 3: 235 peptides, 33 chains. Longest chain 20 peptides. Score 0.460 Round 4: 224 peptides, 29 chains. Longest chain 20 peptides. Score 0.477 Round 5: 231 peptides, 29 chains. Longest chain 20 peptides. Score 0.493 Taking the results from Round 5 Chains 29, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6823 restraints for refining 3018 atoms. 6044 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2536 (Rfree = 0.000) for 3018 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.2540 (Rfree = 0.000) for 2991 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 38: After refmac, R = 0.2371 (Rfree = 0.000) for 2965 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2392 (Rfree = 0.000) for 2956 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 40: After refmac, R = 0.2257 (Rfree = 0.000) for 2948 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.06 Search for helices and strands: 0 residues in 0 chains, 3085 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3103 seeds are put forward Round 1: 195 peptides, 37 chains. Longest chain 12 peptides. Score 0.310 Round 2: 213 peptides, 33 chains. Longest chain 16 peptides. Score 0.405 Round 3: 225 peptides, 33 chains. Longest chain 14 peptides. Score 0.436 Round 4: 234 peptides, 32 chains. Longest chain 21 peptides. Score 0.468 Round 5: 234 peptides, 31 chains. Longest chain 21 peptides. Score 0.479 Taking the results from Round 5 Chains 31, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5718 reflections ( 98.03 % complete ) and 6865 restraints for refining 3020 atoms. 6084 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2511 (Rfree = 0.000) for 3020 atoms. Found 9 (14 requested) and removed 10 (7 requested) atoms. Cycle 42: After refmac, R = 0.2214 (Rfree = 0.000) for 2997 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.2245 (Rfree = 0.000) for 2980 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.2181 (Rfree = 0.000) for 2971 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 45: After refmac, R = 0.2177 (Rfree = 0.000) for 2968 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3093 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3111 seeds are put forward Round 1: 185 peptides, 35 chains. Longest chain 11 peptides. Score 0.306 Round 2: 228 peptides, 33 chains. Longest chain 20 peptides. Score 0.443 Round 3: 218 peptides, 33 chains. Longest chain 15 peptides. Score 0.418 Round 4: 229 peptides, 32 chains. Longest chain 18 peptides. Score 0.456 Round 5: 221 peptides, 30 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 191, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5718 reflections ( 98.03 % complete ) and 6889 restraints for refining 3019 atoms. 6155 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2378 (Rfree = 0.000) for 3019 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2342 (Rfree = 0.000) for 2986 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2363 (Rfree = 0.000) for 2966 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2191 (Rfree = 0.000) for 2947 atoms. TimeTaking 36.88