null Sun 23 Dec 22:23:10 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 2fea-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fea-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fea-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-4.0-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/2fea-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-4.0-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 22:23:20 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/2fea-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-4.0-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6600 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-4.0-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3776 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: 22.949 4.000 Wilson plot Bfac: 84.85 4735 reflections ( 98.16 % complete ) and 0 restraints for refining 4170 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3464 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3557 (Rfree = 0.000) for 4170 atoms. Found 19 (19 requested) and removed 50 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 4200 seeds are put forward NCS extension: 0 residues added, 4200 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 8 peptides. Score 0.247 Round 2: 183 peptides, 33 chains. Longest chain 12 peptides. Score 0.344 Round 3: 199 peptides, 35 chains. Longest chain 15 peptides. Score 0.367 Round 4: 206 peptides, 33 chains. Longest chain 13 peptides. Score 0.414 Round 5: 212 peptides, 33 chains. Longest chain 26 peptides. Score 0.431 Taking the results from Round 5 Chains 33, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 8233 restraints for refining 3410 atoms. 7550 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2898 (Rfree = 0.000) for 3410 atoms. Found 7 (16 requested) and removed 26 (8 requested) atoms. Cycle 2: After refmac, R = 0.2738 (Rfree = 0.000) for 3335 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 3: After refmac, R = 0.2579 (Rfree = 0.000) for 3291 atoms. Found 13 (15 requested) and removed 22 (7 requested) atoms. Cycle 4: After refmac, R = 0.2658 (Rfree = 0.000) for 3255 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 5: After refmac, R = 0.2057 (Rfree = 0.000) for 3224 atoms. Found 4 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 3334 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 3367 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 10 peptides. Score 0.297 Round 2: 210 peptides, 38 chains. Longest chain 12 peptides. Score 0.361 Round 3: 231 peptides, 38 chains. Longest chain 15 peptides. Score 0.423 Round 4: 225 peptides, 35 chains. Longest chain 14 peptides. Score 0.443 Round 5: 225 peptides, 36 chains. Longest chain 21 peptides. Score 0.431 Taking the results from Round 4 Chains 35, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7566 restraints for refining 3266 atoms. 6841 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2287 (Rfree = 0.000) for 3266 atoms. Found 6 (15 requested) and removed 32 (7 requested) atoms. Cycle 7: After refmac, R = 0.2432 (Rfree = 0.000) for 3207 atoms. Found 15 (15 requested) and removed 48 (7 requested) atoms. Cycle 8: After refmac, R = 0.2274 (Rfree = 0.000) for 3147 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 9: After refmac, R = 0.2283 (Rfree = 0.000) for 3107 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 10: After refmac, R = 0.2193 (Rfree = 0.000) for 3077 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 3240 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3259 seeds are put forward Round 1: 189 peptides, 39 chains. Longest chain 9 peptides. Score 0.281 Round 2: 235 peptides, 40 chains. Longest chain 12 peptides. Score 0.410 Round 3: 237 peptides, 36 chains. Longest chain 18 peptides. Score 0.464 Round 4: 245 peptides, 39 chains. Longest chain 15 peptides. Score 0.450 Round 5: 232 peptides, 32 chains. Longest chain 17 peptides. Score 0.498 Taking the results from Round 5 Chains 32, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7550 restraints for refining 3301 atoms. 6782 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 3301 atoms. Found 10 (15 requested) and removed 33 (7 requested) atoms. Cycle 12: After refmac, R = 0.2170 (Rfree = 0.000) for 3241 atoms. Found 15 (15 requested) and removed 28 (7 requested) atoms. Cycle 13: After refmac, R = 0.2189 (Rfree = 0.000) for 3215 atoms. Found 12 (15 requested) and removed 24 (7 requested) atoms. Cycle 14: After refmac, R = 0.2205 (Rfree = 0.000) for 3187 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 15: After refmac, R = 0.1723 (Rfree = 0.000) for 3175 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 3298 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3315 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 10 peptides. Score 0.300 Round 2: 206 peptides, 36 chains. Longest chain 11 peptides. Score 0.375 Round 3: 205 peptides, 34 chains. Longest chain 14 peptides. Score 0.398 Round 4: 198 peptides, 33 chains. Longest chain 13 peptides. Score 0.390 Round 5: 207 peptides, 34 chains. Longest chain 16 peptides. Score 0.404 Taking the results from Round 5 Chains 34, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7793 restraints for refining 3306 atoms. 7135 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2238 (Rfree = 0.000) for 3306 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 17: After refmac, R = 0.2113 (Rfree = 0.000) for 3268 atoms. Found 10 (15 requested) and removed 24 (7 requested) atoms. Cycle 18: After refmac, R = 0.2113 (Rfree = 0.000) for 3244 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 19: After refmac, R = 0.2098 (Rfree = 0.000) for 3233 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 20: After refmac, R = 0.1998 (Rfree = 0.000) for 3227 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 3335 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3354 seeds are put forward Round 1: 186 peptides, 37 chains. Longest chain 10 peptides. Score 0.299 Round 2: 204 peptides, 36 chains. Longest chain 12 peptides. Score 0.369 Round 3: 212 peptides, 36 chains. Longest chain 15 peptides. Score 0.393 Round 4: 213 peptides, 35 chains. Longest chain 13 peptides. Score 0.409 Round 5: 203 peptides, 31 chains. Longest chain 13 peptides. Score 0.431 Taking the results from Round 5 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 8002 restraints for refining 3410 atoms. 7331 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2374 (Rfree = 0.000) for 3410 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 22: After refmac, R = 0.2125 (Rfree = 0.000) for 3378 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 23: After refmac, R = 0.2003 (Rfree = 0.000) for 3357 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 24: After refmac, R = 0.2103 (Rfree = 0.000) for 3333 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 25: After refmac, R = 0.2001 (Rfree = 0.000) for 3318 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3462 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3478 seeds are put forward Round 1: 158 peptides, 32 chains. Longest chain 8 peptides. Score 0.276 Round 2: 176 peptides, 32 chains. Longest chain 11 peptides. Score 0.336 Round 3: 193 peptides, 33 chains. Longest chain 15 peptides. Score 0.375 Round 4: 187 peptides, 31 chains. Longest chain 14 peptides. Score 0.384 Round 5: 202 peptides, 33 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 5 Chains 33, Residues 169, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7985 restraints for refining 3410 atoms. 7315 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2332 (Rfree = 0.000) for 3410 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.2061 (Rfree = 0.000) for 3381 atoms. Found 13 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.1720 (Rfree = 0.000) for 3361 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.1584 (Rfree = 0.000) for 3349 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.1560 (Rfree = 0.000) for 3335 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 3445 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3461 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 6 peptides. Score 0.238 Round 2: 170 peptides, 33 chains. Longest chain 10 peptides. Score 0.302 Round 3: 172 peptides, 32 chains. Longest chain 10 peptides. Score 0.323 Round 4: 170 peptides, 31 chains. Longest chain 9 peptides. Score 0.330 Round 5: 153 peptides, 26 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 5 Chains 26, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 8279 restraints for refining 3410 atoms. 7797 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2474 (Rfree = 0.000) for 3410 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 32: After refmac, R = 0.2274 (Rfree = 0.000) for 3380 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 33: After refmac, R = 0.2177 (Rfree = 0.000) for 3363 atoms. Found 12 (16 requested) and removed 19 (8 requested) atoms. Cycle 34: After refmac, R = 0.2248 (Rfree = 0.000) for 3340 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 35: After refmac, R = 0.2068 (Rfree = 0.000) for 3321 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 3436 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 3438 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 8 peptides. Score 0.236 Round 2: 142 peptides, 27 chains. Longest chain 10 peptides. Score 0.295 Round 3: 152 peptides, 29 chains. Longest chain 9 peptides. Score 0.299 Round 4: 159 peptides, 30 chains. Longest chain 11 peptides. Score 0.308 Round 5: 174 peptides, 31 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 5 Chains 31, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7908 restraints for refining 3356 atoms. 7367 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2315 (Rfree = 0.000) for 3356 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 37: After refmac, R = 0.2052 (Rfree = 0.000) for 3321 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 38: After refmac, R = 0.2123 (Rfree = 0.000) for 3300 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 39: After refmac, R = 0.1461 (Rfree = 0.000) for 3290 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.1393 (Rfree = 0.000) for 3279 atoms. Found 0 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 3372 seeds are put forward NCS extension: 0 residues added, 3372 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 9 peptides. Score 0.249 Round 2: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.296 Round 3: 170 peptides, 29 chains. Longest chain 12 peptides. Score 0.358 Round 4: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.341 Round 5: 162 peptides, 29 chains. Longest chain 9 peptides. Score 0.333 Taking the results from Round 3 Chains 29, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4735 reflections ( 98.16 % complete ) and 7613 restraints for refining 3305 atoms. 7078 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1956 (Rfree = 0.000) for 3305 atoms. Found 9 (15 requested) and removed 25 (7 requested) atoms. Cycle 42: After refmac, R = 0.2004 (Rfree = 0.000) for 3277 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 43: After refmac, R = 0.2065 (Rfree = 0.000) for 3271 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 44: After refmac, R = 0.1920 (Rfree = 0.000) for 3262 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 45: After refmac, R = 0.1446 (Rfree = 0.000) for 3250 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 3362 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3382 seeds are put forward Round 1: 139 peptides, 31 chains. Longest chain 8 peptides. Score 0.224 Round 2: 165 peptides, 33 chains. Longest chain 8 peptides. Score 0.285 Round 3: 155 peptides, 32 chains. Longest chain 8 peptides. Score 0.266 Round 4: 155 peptides, 30 chains. Longest chain 10 peptides. Score 0.295 Round 5: 156 peptides, 31 chains. Longest chain 10 peptides. Score 0.284 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 125, 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 2fea-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4735 reflections ( 98.16 % complete ) and 7907 restraints for refining 3357 atoms. 7437 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2445 (Rfree = 0.000) for 3357 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2016 (Rfree = 0.000) for 3333 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2031 (Rfree = 0.000) for 3320 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2050 (Rfree = 0.000) for 3308 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:15:23 GMT 2018 Job finished. TimeTaking 52.21 Used memory is bytes: 5512528