Mon 24 Dec 07:49:31 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 1vqs-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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/1vqs-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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 07:49:36 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/1vqs-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-4.0-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 449 and 0 Target number of residues in the AU: 449 Target solvent content: 0.6429 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-4.0-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 4.000 Wilson plot Bfac: 73.36 6209 reflections ( 99.41 % complete ) and 0 restraints for refining 5135 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3508 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3355 (Rfree = 0.000) for 5135 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 0 residues added, 5223 seeds are put forward Round 1: 197 peptides, 40 chains. Longest chain 9 peptides. Score 0.276 Round 2: 255 peptides, 42 chains. Longest chain 15 peptides. Score 0.402 Round 3: 294 peptides, 44 chains. Longest chain 15 peptides. Score 0.471 Round 4: 308 peptides, 41 chains. Longest chain 21 peptides. Score 0.529 Round 5: 309 peptides, 43 chains. Longest chain 15 peptides. Score 0.512 Taking the results from Round 4 Chains 41, Residues 267, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9622 restraints for refining 4189 atoms. 8595 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2883 (Rfree = 0.000) for 4189 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 2: After refmac, R = 0.2764 (Rfree = 0.000) for 4058 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.2623 (Rfree = 0.000) for 3984 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 4: After refmac, R = 0.2478 (Rfree = 0.000) for 3935 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 5: After refmac, R = 0.2460 (Rfree = 0.000) for 3897 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 4025 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 4065 seeds are put forward Round 1: 255 peptides, 48 chains. Longest chain 10 peptides. Score 0.339 Round 2: 293 peptides, 44 chains. Longest chain 16 peptides. Score 0.469 Round 3: 319 peptides, 51 chains. Longest chain 13 peptides. Score 0.459 Round 4: 317 peptides, 44 chains. Longest chain 15 peptides. Score 0.520 Round 5: 325 peptides, 45 chains. Longest chain 14 peptides. Score 0.527 Taking the results from Round 5 Chains 45, Residues 280, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 8968 restraints for refining 4077 atoms. 7837 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2451 (Rfree = 0.000) for 4077 atoms. Found 17 (19 requested) and removed 30 (9 requested) atoms. Cycle 7: After refmac, R = 0.2213 (Rfree = 0.000) for 4017 atoms. Found 7 (19 requested) and removed 30 (9 requested) atoms. Cycle 8: After refmac, R = 0.2228 (Rfree = 0.000) for 3973 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 9: After refmac, R = 0.2191 (Rfree = 0.000) for 3944 atoms. Found 15 (18 requested) and removed 16 (9 requested) atoms. Cycle 10: After refmac, R = 0.2173 (Rfree = 0.000) for 3930 atoms. Found 15 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 4056 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4074 seeds are put forward Round 1: 264 peptides, 47 chains. Longest chain 12 peptides. Score 0.372 Round 2: 310 peptides, 47 chains. Longest chain 18 peptides. Score 0.477 Round 3: 302 peptides, 44 chains. Longest chain 21 peptides. Score 0.488 Round 4: 303 peptides, 42 chains. Longest chain 17 peptides. Score 0.509 Round 5: 314 peptides, 43 chains. Longest chain 19 peptides. Score 0.523 Taking the results from Round 5 Chains 43, Residues 271, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9501 restraints for refining 4148 atoms. 8460 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2535 (Rfree = 0.000) for 4148 atoms. Found 19 (19 requested) and removed 46 (9 requested) atoms. Cycle 12: After refmac, R = 0.2325 (Rfree = 0.000) for 4084 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 13: After refmac, R = 0.2254 (Rfree = 0.000) for 4050 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. Cycle 14: After refmac, R = 0.2285 (Rfree = 0.000) for 4011 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 15: After refmac, R = 0.2320 (Rfree = 0.000) for 3980 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 4120 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 4135 seeds are put forward Round 1: 231 peptides, 48 chains. Longest chain 8 peptides. Score 0.277 Round 2: 288 peptides, 42 chains. Longest chain 15 peptides. Score 0.477 Round 3: 277 peptides, 41 chains. Longest chain 13 peptides. Score 0.463 Round 4: 302 peptides, 46 chains. Longest chain 13 peptides. Score 0.469 Round 5: 308 peptides, 46 chains. Longest chain 13 peptides. Score 0.482 Taking the results from Round 5 Chains 46, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9565 restraints for refining 4189 atoms. 8563 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2409 (Rfree = 0.000) for 4189 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 17: After refmac, R = 0.2363 (Rfree = 0.000) for 4133 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. Cycle 18: After refmac, R = 0.2296 (Rfree = 0.000) for 4081 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 19: After refmac, R = 0.2156 (Rfree = 0.000) for 4056 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2249 (Rfree = 0.000) for 4044 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 4203 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4216 seeds are put forward Round 1: 245 peptides, 47 chains. Longest chain 10 peptides. Score 0.324 Round 2: 288 peptides, 43 chains. Longest chain 15 peptides. Score 0.468 Round 3: 321 peptides, 50 chains. Longest chain 19 peptides. Score 0.473 Round 4: 305 peptides, 49 chains. Longest chain 15 peptides. Score 0.447 Round 5: 301 peptides, 43 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 5 Chains 43, Residues 258, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9725 restraints for refining 4190 atoms. 8736 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2557 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Cycle 22: After refmac, R = 0.2458 (Rfree = 0.000) for 4127 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 23: After refmac, R = 0.2227 (Rfree = 0.000) for 4086 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 24: After refmac, R = 0.1910 (Rfree = 0.000) for 4067 atoms. Found 5 (19 requested) and removed 18 (9 requested) atoms. Cycle 25: After refmac, R = 0.1807 (Rfree = 0.000) for 4037 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 4147 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4159 seeds are put forward Round 1: 250 peptides, 48 chains. Longest chain 10 peptides. Score 0.326 Round 2: 288 peptides, 46 chains. Longest chain 18 peptides. Score 0.438 Round 3: 269 peptides, 44 chains. Longest chain 16 peptides. Score 0.415 Round 4: 257 peptides, 42 chains. Longest chain 14 peptides. Score 0.407 Round 5: 264 peptides, 40 chains. Longest chain 22 peptides. Score 0.444 Taking the results from Round 5 Chains 42, Residues 224, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9806 restraints for refining 4190 atoms. 8916 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2442 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. Cycle 27: After refmac, R = 0.2367 (Rfree = 0.000) for 4134 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 28: After refmac, R = 0.2327 (Rfree = 0.000) for 4101 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 29: After refmac, R = 0.1819 (Rfree = 0.000) for 4074 atoms. Found 11 (19 requested) and removed 17 (9 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 4051 atoms. Found 8 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 4166 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 4201 seeds are put forward Round 1: 203 peptides, 43 chains. Longest chain 8 peptides. Score 0.257 Round 2: 256 peptides, 43 chains. Longest chain 14 peptides. Score 0.394 Round 3: 245 peptides, 38 chains. Longest chain 15 peptides. Score 0.420 Round 4: 273 peptides, 43 chains. Longest chain 14 peptides. Score 0.434 Round 5: 246 peptides, 37 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 4 Chains 43, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9826 restraints for refining 4168 atoms. 8949 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2241 (Rfree = 0.000) for 4168 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 32: After refmac, R = 0.2354 (Rfree = 0.000) for 4133 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 33: After refmac, R = 0.2129 (Rfree = 0.000) for 4101 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 34: After refmac, R = 0.2031 (Rfree = 0.000) for 4075 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 35: After refmac, R = 0.1998 (Rfree = 0.000) for 4059 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 4182 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4199 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 8 peptides. Score 0.281 Round 2: 215 peptides, 39 chains. Longest chain 11 peptides. Score 0.335 Round 3: 215 peptides, 40 chains. Longest chain 8 peptides. Score 0.324 Round 4: 217 peptides, 37 chains. Longest chain 11 peptides. Score 0.363 Round 5: 219 peptides, 39 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 4 Chains 37, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 10097 restraints for refining 4190 atoms. 9414 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2282 (Rfree = 0.000) for 4190 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 37: After refmac, R = 0.2239 (Rfree = 0.000) for 4154 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 38: After refmac, R = 0.2197 (Rfree = 0.000) for 4131 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.2154 (Rfree = 0.000) for 4116 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 40: After refmac, R = 0.2144 (Rfree = 0.000) for 4096 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 4209 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 4219 seeds are put forward Round 1: 181 peptides, 40 chains. Longest chain 7 peptides. Score 0.230 Round 2: 220 peptides, 43 chains. Longest chain 12 peptides. Score 0.303 Round 3: 221 peptides, 43 chains. Longest chain 9 peptides. Score 0.306 Round 4: 232 peptides, 45 chains. Longest chain 11 peptides. Score 0.313 Round 5: 228 peptides, 41 chains. Longest chain 13 peptides. Score 0.346 Taking the results from Round 5 Chains 41, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6209 reflections ( 99.41 % complete ) and 9834 restraints for refining 4148 atoms. 9127 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2269 (Rfree = 0.000) for 4148 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 42: After refmac, R = 0.2236 (Rfree = 0.000) for 4107 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 43: After refmac, R = 0.1723 (Rfree = 0.000) for 4086 atoms. Found 18 (19 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1931 (Rfree = 0.000) for 4078 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 45: After refmac, R = 0.1633 (Rfree = 0.000) for 4065 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 4174 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4188 seeds are put forward Round 1: 159 peptides, 34 chains. Longest chain 8 peptides. Score 0.239 Round 2: 218 peptides, 43 chains. Longest chain 10 peptides. Score 0.298 Round 3: 234 peptides, 44 chains. Longest chain 10 peptides. Score 0.329 Round 4: 225 peptides, 45 chains. Longest chain 10 peptides. Score 0.294 Round 5: 228 peptides, 44 chains. Longest chain 11 peptides. Score 0.313 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 190, 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 1vqs-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6209 reflections ( 99.41 % complete ) and 9563 restraints for refining 4063 atoms. 8847 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2097 (Rfree = 0.000) for 4063 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2171 (Rfree = 0.000) for 4025 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2183 (Rfree = 0.000) for 4001 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2134 (Rfree = 0.000) for 3980 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 52.68