null Sun 23 Dec 22:22:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2a6a-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-parrot-hancs ############### 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 22:23:04 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/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-parrot-hancs/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 317 and 0 Target number of residues in the AU: 317 Target solvent content: 0.6743 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-3.8-parrot-hancs.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-3.8-parrot-hancs.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 3.800 Wilson plot Bfac: 95.98 5455 reflections ( 98.61 % complete ) and 0 restraints for refining 3867 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3499 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2590 (Rfree = 0.000) for 3867 atoms. Found 17 (21 requested) and removed 478 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 3441 seeds are put forward NCS extension: 0 residues added, 3441 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 11 peptides. Score 0.314 Round 2: 206 peptides, 34 chains. Longest chain 14 peptides. Score 0.409 Round 3: 212 peptides, 32 chains. Longest chain 15 peptides. Score 0.453 Round 4: 215 peptides, 33 chains. Longest chain 19 peptides. Score 0.449 Round 5: 209 peptides, 30 chains. Longest chain 20 peptides. Score 0.470 Taking the results from Round 5 Chains 30, Residues 179, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6737 restraints for refining 2999 atoms. 6021 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 2999 atoms. Found 16 (16 requested) and removed 54 (8 requested) atoms. Cycle 2: After refmac, R = 0.2307 (Rfree = 0.000) for 2918 atoms. Found 9 (16 requested) and removed 18 (8 requested) atoms. Cycle 3: After refmac, R = 0.2214 (Rfree = 0.000) for 2897 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2142 (Rfree = 0.000) for 2885 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2139 (Rfree = 0.000) for 2869 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.50 Search for helices and strands: 0 residues in 0 chains, 3016 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 3051 seeds are put forward Round 1: 215 peptides, 35 chains. Longest chain 20 peptides. Score 0.423 Round 2: 243 peptides, 33 chains. Longest chain 17 peptides. Score 0.526 Round 3: 248 peptides, 30 chains. Longest chain 21 peptides. Score 0.572 Round 4: 232 peptides, 31 chains. Longest chain 19 peptides. Score 0.520 Round 5: 244 peptides, 30 chains. Longest chain 20 peptides. Score 0.563 Taking the results from Round 3 Chains 32, Residues 218, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6833 restraints for refining 3059 atoms. 5962 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2384 (Rfree = 0.000) for 3059 atoms. Found 15 (16 requested) and removed 25 (8 requested) atoms. Cycle 7: After refmac, R = 0.2181 (Rfree = 0.000) for 3012 atoms. Found 7 (16 requested) and removed 19 (8 requested) atoms. Cycle 8: After refmac, R = 0.2376 (Rfree = 0.000) for 2989 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.2079 (Rfree = 0.000) for 2966 atoms. Found 11 (16 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2154 (Rfree = 0.000) for 2949 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.55 Search for helices and strands: 0 residues in 0 chains, 3124 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3142 seeds are put forward Round 1: 203 peptides, 34 chains. Longest chain 13 peptides. Score 0.400 Round 2: 230 peptides, 30 chains. Longest chain 16 peptides. Score 0.527 Round 3: 236 peptides, 32 chains. Longest chain 19 peptides. Score 0.519 Round 4: 241 peptides, 30 chains. Longest chain 20 peptides. Score 0.555 Round 5: 233 peptides, 27 chains. Longest chain 17 peptides. Score 0.569 Taking the results from Round 5 Chains 29, Residues 206, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6908 restraints for refining 3117 atoms. 6064 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2303 (Rfree = 0.000) for 3117 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 3080 atoms. Found 10 (17 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.2074 (Rfree = 0.000) for 3059 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.2101 (Rfree = 0.000) for 3050 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.2725 (Rfree = 0.000) for 3031 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.54 Search for helices and strands: 0 residues in 0 chains, 3177 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3192 seeds are put forward Round 1: 170 peptides, 29 chains. Longest chain 16 peptides. Score 0.364 Round 2: 216 peptides, 30 chains. Longest chain 20 peptides. Score 0.489 Round 3: 226 peptides, 28 chains. Longest chain 32 peptides. Score 0.540 Round 4: 227 peptides, 31 chains. Longest chain 18 peptides. Score 0.507 Round 5: 226 peptides, 28 chains. Longest chain 37 peptides. Score 0.540 Taking the results from Round 5 Chains 30, Residues 198, Estimated correctness of the model 0.0 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6924 restraints for refining 3155 atoms. 6035 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2184 (Rfree = 0.000) for 3155 atoms. Found 16 (17 requested) and removed 29 (8 requested) atoms. Cycle 17: After refmac, R = 0.1979 (Rfree = 0.000) for 3121 atoms. Found 7 (17 requested) and removed 18 (8 requested) atoms. Cycle 18: After refmac, R = 0.1894 (Rfree = 0.000) for 3101 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.1838 (Rfree = 0.000) for 3089 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1808 (Rfree = 0.000) for 3078 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.58 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 44 residues added (7 deleted due to clashes), 3234 seeds are put forward Round 1: 213 peptides, 32 chains. Longest chain 14 peptides. Score 0.456 Round 2: 230 peptides, 27 chains. Longest chain 18 peptides. Score 0.562 Round 3: 229 peptides, 29 chains. Longest chain 18 peptides. Score 0.536 Round 4: 223 peptides, 28 chains. Longest chain 32 peptides. Score 0.533 Round 5: 234 peptides, 30 chains. Longest chain 23 peptides. Score 0.537 Taking the results from Round 2 Chains 28, Residues 203, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7052 restraints for refining 3155 atoms. 6216 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2320 (Rfree = 0.000) for 3155 atoms. Found 12 (17 requested) and removed 65 (8 requested) atoms. Cycle 22: After refmac, R = 0.2012 (Rfree = 0.000) for 3091 atoms. Found 3 (17 requested) and removed 26 (8 requested) atoms. Cycle 23: After refmac, R = 0.2276 (Rfree = 0.000) for 3058 atoms. Found 13 (16 requested) and removed 23 (8 requested) atoms. Cycle 24: After refmac, R = 0.2051 (Rfree = 0.000) for 3038 atoms. Found 14 (16 requested) and removed 30 (8 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 3008 atoms. Found 11 (16 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.54 Search for helices and strands: 0 residues in 0 chains, 3092 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3115 seeds are put forward Round 1: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.371 Round 2: 208 peptides, 32 chains. Longest chain 12 peptides. Score 0.441 Round 3: 227 peptides, 31 chains. Longest chain 26 peptides. Score 0.507 Round 4: 214 peptides, 29 chains. Longest chain 15 peptides. Score 0.496 Round 5: 222 peptides, 29 chains. Longest chain 15 peptides. Score 0.518 Taking the results from Round 5 Chains 29, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7261 restraints for refining 3150 atoms. 6518 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2234 (Rfree = 0.000) for 3150 atoms. Found 13 (17 requested) and removed 51 (8 requested) atoms. Cycle 27: After refmac, R = 0.2376 (Rfree = 0.000) for 3094 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 28: After refmac, R = 0.2275 (Rfree = 0.000) for 3077 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 29: After refmac, R = 0.2213 (Rfree = 0.000) for 3053 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 30: After refmac, R = 0.2206 (Rfree = 0.000) for 3042 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.55 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3208 seeds are put forward Round 1: 177 peptides, 30 chains. Longest chain 17 peptides. Score 0.373 Round 2: 221 peptides, 34 chains. Longest chain 15 peptides. Score 0.453 Round 3: 219 peptides, 31 chains. Longest chain 12 peptides. Score 0.485 Round 4: 221 peptides, 32 chains. Longest chain 18 peptides. Score 0.478 Round 5: 215 peptides, 28 chains. Longest chain 24 peptides. Score 0.511 Taking the results from Round 5 Chains 30, Residues 187, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7086 restraints for refining 3155 atoms. 6335 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2323 (Rfree = 0.000) for 3155 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 32: After refmac, R = 0.2248 (Rfree = 0.000) for 3126 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 33: After refmac, R = 0.2069 (Rfree = 0.000) for 3103 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 34: After refmac, R = 0.2374 (Rfree = 0.000) for 3083 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 35: After refmac, R = 0.2137 (Rfree = 0.000) for 3062 atoms. Found 15 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.55 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3215 seeds are put forward Round 1: 163 peptides, 35 chains. Longest chain 7 peptides. Score 0.253 Round 2: 181 peptides, 29 chains. Longest chain 16 peptides. Score 0.399 Round 3: 196 peptides, 33 chains. Longest chain 11 peptides. Score 0.391 Round 4: 198 peptides, 28 chains. Longest chain 12 peptides. Score 0.464 Round 5: 192 peptides, 28 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 4 Chains 28, Residues 170, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7094 restraints for refining 3145 atoms. 6406 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2518 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 97 (8 requested) atoms. Cycle 37: After refmac, R = 0.2426 (Rfree = 0.000) for 3048 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 38: After refmac, R = 0.2333 (Rfree = 0.000) for 3016 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 39: After refmac, R = 0.2278 (Rfree = 0.000) for 3002 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 40: After refmac, R = 0.2492 (Rfree = 0.000) for 2986 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.86 3.61 Search for helices and strands: 0 residues in 0 chains, 3123 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3137 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 10 peptides. Score 0.257 Round 2: 190 peptides, 34 chains. Longest chain 12 peptides. Score 0.359 Round 3: 182 peptides, 30 chains. Longest chain 14 peptides. Score 0.389 Round 4: 183 peptides, 27 chains. Longest chain 17 peptides. Score 0.433 Round 5: 186 peptides, 29 chains. Longest chain 16 peptides. Score 0.415 Taking the results from Round 4 Chains 27, Residues 156, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6927 restraints for refining 3063 atoms. 6300 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2567 (Rfree = 0.000) for 3063 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 42: After refmac, R = 0.2182 (Rfree = 0.000) for 3025 atoms. Found 8 (16 requested) and removed 31 (8 requested) atoms. Cycle 43: After refmac, R = 0.1831 (Rfree = 0.000) for 2993 atoms. Found 3 (16 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.1755 (Rfree = 0.000) for 2974 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. Cycle 45: After refmac, R = 0.1814 (Rfree = 0.000) for 2964 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.58 Search for helices and strands: 0 residues in 0 chains, 3068 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3088 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 13 peptides. Score 0.257 Round 2: 190 peptides, 35 chains. Longest chain 14 peptides. Score 0.345 Round 3: 185 peptides, 33 chains. Longest chain 12 peptides. Score 0.356 Round 4: 193 peptides, 33 chains. Longest chain 12 peptides. Score 0.382 Round 5: 188 peptides, 31 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 157, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5455 reflections ( 98.61 % complete ) and 7187 restraints for refining 3095 atoms. 6569 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2171 (Rfree = 0.000) for 3095 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2277 (Rfree = 0.000) for 3078 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2208 (Rfree = 0.000) for 3060 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2233 (Rfree = 0.000) for 3034 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:49 GMT 2018 Job finished. TimeTaking 55.9 Used memory is bytes: 10226720