Mon 24 Dec 00:45:10 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 2a6a-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-3.4-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/2a6a-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-3.4-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 00:45:14 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/2a6a-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-3.4-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 330 and 0 Target number of residues in the AU: 330 Target solvent content: 0.6609 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-3.4-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3488 target number of atoms Had to go as low as 0.70 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: 108.588 3.400 Wilson plot Bfac: 85.40 7577 reflections ( 98.98 % complete ) and 0 restraints for refining 3876 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3454 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3300 (Rfree = 0.000) for 3876 atoms. Found 29 (29 requested) and removed 61 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.32 Search for helices and strands: 0 residues in 0 chains, 3922 seeds are put forward NCS extension: 0 residues added, 3922 seeds are put forward Round 1: 194 peptides, 32 chains. Longest chain 18 peptides. Score 0.399 Round 2: 227 peptides, 32 chains. Longest chain 16 peptides. Score 0.495 Round 3: 230 peptides, 31 chains. Longest chain 18 peptides. Score 0.515 Round 4: 249 peptides, 35 chains. Longest chain 14 peptides. Score 0.518 Round 5: 248 peptides, 32 chains. Longest chain 17 peptides. Score 0.550 Taking the results from Round 5 Chains 32, Residues 216, Estimated correctness of the model 11.5 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 7194 restraints for refining 3167 atoms. 6316 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2668 (Rfree = 0.000) for 3167 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 2: After refmac, R = 0.2272 (Rfree = 0.000) for 3114 atoms. Found 19 (23 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2051 (Rfree = 0.000) for 3083 atoms. Found 11 (23 requested) and removed 21 (11 requested) atoms. Cycle 4: After refmac, R = 0.1976 (Rfree = 0.000) for 3058 atoms. Found 14 (23 requested) and removed 29 (11 requested) atoms. Cycle 5: After refmac, R = 0.2350 (Rfree = 0.000) for 3037 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3181 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3199 seeds are put forward Round 1: 229 peptides, 37 chains. Longest chain 20 peptides. Score 0.438 Round 2: 241 peptides, 34 chains. Longest chain 18 peptides. Score 0.509 Round 3: 257 peptides, 35 chains. Longest chain 20 peptides. Score 0.539 Round 4: 265 peptides, 30 chains. Longest chain 22 peptides. Score 0.612 Round 5: 251 peptides, 28 chains. Longest chain 20 peptides. Score 0.601 Taking the results from Round 4 Chains 32, Residues 235, Estimated correctness of the model 32.5 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6626 restraints for refining 3171 atoms. 5558 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2441 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 7: After refmac, R = 0.2229 (Rfree = 0.000) for 3138 atoms. Found 18 (23 requested) and removed 20 (11 requested) atoms. Cycle 8: After refmac, R = 0.2100 (Rfree = 0.000) for 3105 atoms. Found 16 (23 requested) and removed 18 (11 requested) atoms. Cycle 9: After refmac, R = 0.2070 (Rfree = 0.000) for 3089 atoms. Found 12 (23 requested) and removed 16 (11 requested) atoms. Cycle 10: After refmac, R = 0.2017 (Rfree = 0.000) for 3076 atoms. Found 13 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3158 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3176 seeds are put forward Round 1: 226 peptides, 31 chains. Longest chain 20 peptides. Score 0.504 Round 2: 266 peptides, 32 chains. Longest chain 25 peptides. Score 0.593 Round 3: 250 peptides, 30 chains. Longest chain 22 peptides. Score 0.577 Round 4: 269 peptides, 28 chains. Longest chain 29 peptides. Score 0.641 Round 5: 268 peptides, 30 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 4 Chains 28, Residues 241, Estimated correctness of the model 41.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6996 restraints for refining 3171 atoms. 6060 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2318 (Rfree = 0.000) for 3171 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. Cycle 12: After refmac, R = 0.2331 (Rfree = 0.000) for 3133 atoms. Found 17 (23 requested) and removed 24 (11 requested) atoms. Cycle 13: After refmac, R = 0.2652 (Rfree = 0.000) for 3102 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 14: After refmac, R = 0.2277 (Rfree = 0.000) for 3080 atoms. Found 20 (23 requested) and removed 25 (11 requested) atoms. Cycle 15: After refmac, R = 0.2627 (Rfree = 0.000) for 3059 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3208 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3231 seeds are put forward Round 1: 223 peptides, 35 chains. Longest chain 15 peptides. Score 0.446 Round 2: 246 peptides, 28 chains. Longest chain 29 peptides. Score 0.590 Round 3: 246 peptides, 27 chains. Longest chain 29 peptides. Score 0.600 Round 4: 252 peptides, 26 chains. Longest chain 30 peptides. Score 0.624 Round 5: 250 peptides, 29 chains. Longest chain 31 peptides. Score 0.588 Taking the results from Round 4 Chains 26, Residues 226, Estimated correctness of the model 36.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6922 restraints for refining 3170 atoms. 6044 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2340 (Rfree = 0.000) for 3170 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 17: After refmac, R = 0.2268 (Rfree = 0.000) for 3149 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 18: After refmac, R = 0.2399 (Rfree = 0.000) for 3116 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 19: After refmac, R = 0.2093 (Rfree = 0.000) for 3080 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 20: After refmac, R = 0.1995 (Rfree = 0.000) for 3080 atoms. Found 12 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3201 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3223 seeds are put forward Round 1: 198 peptides, 30 chains. Longest chain 18 peptides. Score 0.438 Round 2: 224 peptides, 28 chains. Longest chain 23 peptides. Score 0.535 Round 3: 235 peptides, 30 chains. Longest chain 20 peptides. Score 0.540 Round 4: 249 peptides, 28 chains. Longest chain 24 peptides. Score 0.597 Round 5: 251 peptides, 28 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 5 Chains 28, Residues 223, Estimated correctness of the model 29.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6824 restraints for refining 3171 atoms. 5910 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2829 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 22: After refmac, R = 0.2245 (Rfree = 0.000) for 3136 atoms. Found 21 (23 requested) and removed 28 (11 requested) atoms. Cycle 23: After refmac, R = 0.2409 (Rfree = 0.000) for 3118 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 24: After refmac, R = 0.2276 (Rfree = 0.000) for 3090 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 25: After refmac, R = 0.2664 (Rfree = 0.000) for 3088 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3250 seeds are put forward Round 1: 227 peptides, 33 chains. Longest chain 15 peptides. Score 0.483 Round 2: 263 peptides, 32 chains. Longest chain 18 peptides. Score 0.586 Round 3: 247 peptides, 23 chains. Longest chain 32 peptides. Score 0.645 Round 4: 238 peptides, 26 chains. Longest chain 23 peptides. Score 0.593 Round 5: 259 peptides, 29 chains. Longest chain 29 peptides. Score 0.609 Taking the results from Round 3 Chains 23, Residues 224, Estimated correctness of the model 42.7 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6443 restraints for refining 3170 atoms. 5392 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2828 (Rfree = 0.000) for 3170 atoms. Found 23 (23 requested) and removed 61 (11 requested) atoms. Cycle 27: After refmac, R = 0.2520 (Rfree = 0.000) for 3103 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 28: After refmac, R = 0.2633 (Rfree = 0.000) for 3082 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 29: After refmac, R = 0.2636 (Rfree = 0.000) for 3061 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 30: After refmac, R = 0.2111 (Rfree = 0.000) for 3039 atoms. Found 18 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.28 Search for helices and strands: 0 residues in 0 chains, 3145 seeds are put forward NCS extension: 28 residues added (11 deleted due to clashes), 3173 seeds are put forward Round 1: 210 peptides, 32 chains. Longest chain 18 peptides. Score 0.447 Round 2: 236 peptides, 27 chains. Longest chain 23 peptides. Score 0.577 Round 3: 222 peptides, 24 chains. Longest chain 22 peptides. Score 0.577 Round 4: 239 peptides, 27 chains. Longest chain 23 peptides. Score 0.584 Round 5: 249 peptides, 25 chains. Longest chain 38 peptides. Score 0.628 Taking the results from Round 5 Chains 29, Residues 224, Estimated correctness of the model 37.5 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6435 restraints for refining 3147 atoms. 5460 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2826 (Rfree = 0.000) for 3147 atoms. Found 23 (23 requested) and removed 59 (11 requested) atoms. Cycle 32: After refmac, R = 0.2379 (Rfree = 0.000) for 3096 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 33: After refmac, R = 0.1977 (Rfree = 0.000) for 3089 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.2144 (Rfree = 0.000) for 3075 atoms. Found 18 (23 requested) and removed 17 (11 requested) atoms. Cycle 35: After refmac, R = 0.2188 (Rfree = 0.000) for 3069 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 3182 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3207 seeds are put forward Round 1: 199 peptides, 31 chains. Longest chain 16 peptides. Score 0.427 Round 2: 249 peptides, 31 chains. Longest chain 18 peptides. Score 0.564 Round 3: 260 peptides, 30 chains. Longest chain 35 peptides. Score 0.601 Round 4: 252 peptides, 28 chains. Longest chain 27 peptides. Score 0.604 Round 5: 245 peptides, 29 chains. Longest chain 34 peptides. Score 0.576 Taking the results from Round 4 Chains 29, Residues 224, Estimated correctness of the model 30.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6699 restraints for refining 3171 atoms. 5767 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2295 (Rfree = 0.000) for 3171 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 37: After refmac, R = 0.2061 (Rfree = 0.000) for 3157 atoms. Found 13 (23 requested) and removed 17 (11 requested) atoms. Cycle 38: After refmac, R = 0.1949 (Rfree = 0.000) for 3142 atoms. Found 12 (23 requested) and removed 15 (11 requested) atoms. Cycle 39: After refmac, R = 0.1887 (Rfree = 0.000) for 3129 atoms. Found 10 (23 requested) and removed 15 (11 requested) atoms. Cycle 40: After refmac, R = 0.2175 (Rfree = 0.000) for 3118 atoms. Found 22 (23 requested) and removed 98 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.29 Search for helices and strands: 0 residues in 0 chains, 3155 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 3185 seeds are put forward Round 1: 195 peptides, 33 chains. Longest chain 18 peptides. Score 0.388 Round 2: 211 peptides, 30 chains. Longest chain 21 peptides. Score 0.475 Round 3: 209 peptides, 30 chains. Longest chain 21 peptides. Score 0.470 Round 4: 226 peptides, 31 chains. Longest chain 22 peptides. Score 0.504 Round 5: 221 peptides, 31 chains. Longest chain 19 peptides. Score 0.491 Taking the results from Round 4 Chains 33, Residues 195, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7577 reflections ( 98.98 % complete ) and 6790 restraints for refining 3160 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3124 (Rfree = 0.000) for 3160 atoms. Found 23 (23 requested) and removed 80 (11 requested) atoms. Cycle 42: After refmac, R = 0.2380 (Rfree = 0.000) for 3079 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 43: After refmac, R = 0.2369 (Rfree = 0.000) for 3063 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 3058 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 45: After refmac, R = 0.2306 (Rfree = 0.000) for 3064 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3186 seeds are put forward Round 1: 191 peptides, 34 chains. Longest chain 14 peptides. Score 0.362 Round 2: 214 peptides, 29 chains. Longest chain 22 peptides. Score 0.496 Round 3: 205 peptides, 28 chains. Longest chain 18 peptides. Score 0.484 Round 4: 214 peptides, 30 chains. Longest chain 16 peptides. Score 0.484 Round 5: 214 peptides, 27 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 187, Estimated correctness of the model 0.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7577 reflections ( 98.98 % complete ) and 7236 restraints for refining 3171 atoms. 6515 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2298 (Rfree = 0.000) for 3171 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2343 (Rfree = 0.000) for 3153 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2211 (Rfree = 0.000) for 3135 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2307 (Rfree = 0.000) for 3116 atoms. TimeTaking 38.98