Sun 23 Dec 23:47:29 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 1z85-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.8-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/1z85-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.8-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 ============================================================ Sun 23 Dec 23:47:34 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/1z85-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.8-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 367 and 0 Target number of residues in the AU: 367 Target solvent content: 0.6554 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-3.8-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: 19 Cell parameters: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.75 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: 65.199 3.800 Wilson plot Bfac: 81.51 6039 reflections ( 99.69 % complete ) and 0 restraints for refining 4131 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3343 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3273 (Rfree = 0.000) for 4131 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.50 Search for helices and strands: 0 residues in 0 chains, 4178 seeds are put forward NCS extension: 0 residues added, 4178 seeds are put forward Round 1: 175 peptides, 32 chains. Longest chain 12 peptides. Score 0.327 Round 2: 259 peptides, 39 chains. Longest chain 14 peptides. Score 0.477 Round 3: 271 peptides, 37 chains. Longest chain 15 peptides. Score 0.528 Round 4: 282 peptides, 34 chains. Longest chain 22 peptides. Score 0.584 Round 5: 264 peptides, 35 chains. Longest chain 15 peptides. Score 0.533 Taking the results from Round 4 Chains 35, Residues 248, Estimated correctness of the model 0.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7089 restraints for refining 3386 atoms. 5988 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2896 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. Cycle 2: After refmac, R = 0.2705 (Rfree = 0.000) for 3295 atoms. Found 16 (18 requested) and removed 34 (9 requested) atoms. Cycle 3: After refmac, R = 0.2733 (Rfree = 0.000) for 3218 atoms. Found 13 (18 requested) and removed 27 (9 requested) atoms. Cycle 4: After refmac, R = 0.2670 (Rfree = 0.000) for 3176 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 5: After refmac, R = 0.2688 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 3282 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3297 seeds are put forward Round 1: 234 peptides, 41 chains. Longest chain 13 peptides. Score 0.387 Round 2: 251 peptides, 36 chains. Longest chain 23 peptides. Score 0.491 Round 3: 273 peptides, 37 chains. Longest chain 16 peptides. Score 0.533 Round 4: 272 peptides, 30 chains. Longest chain 18 peptides. Score 0.602 Round 5: 271 peptides, 34 chains. Longest chain 18 peptides. Score 0.560 Taking the results from Round 4 Chains 30, Residues 242, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7327 restraints for refining 3386 atoms. 6389 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2734 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 7: After refmac, R = 0.2753 (Rfree = 0.000) for 3339 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 8: After refmac, R = 0.2654 (Rfree = 0.000) for 3294 atoms. Found 18 (18 requested) and removed 40 (9 requested) atoms. Cycle 9: After refmac, R = 0.2631 (Rfree = 0.000) for 3230 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 10: After refmac, R = 0.2739 (Rfree = 0.000) for 3206 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 3345 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3360 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 12 peptides. Score 0.347 Round 2: 239 peptides, 34 chains. Longest chain 14 peptides. Score 0.483 Round 3: 257 peptides, 35 chains. Longest chain 15 peptides. Score 0.516 Round 4: 256 peptides, 34 chains. Longest chain 16 peptides. Score 0.525 Round 5: 262 peptides, 31 chains. Longest chain 16 peptides. Score 0.570 Taking the results from Round 5 Chains 31, Residues 231, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7281 restraints for refining 3371 atoms. 6354 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2735 (Rfree = 0.000) for 3371 atoms. Found 18 (18 requested) and removed 38 (9 requested) atoms. Cycle 12: After refmac, R = 0.2612 (Rfree = 0.000) for 3319 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 13: After refmac, R = 0.2581 (Rfree = 0.000) for 3274 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 14: After refmac, R = 0.2628 (Rfree = 0.000) for 3255 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 15: After refmac, R = 0.2505 (Rfree = 0.000) for 3246 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 3369 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3389 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 10 peptides. Score 0.333 Round 2: 247 peptides, 39 chains. Longest chain 13 peptides. Score 0.446 Round 3: 262 peptides, 32 chains. Longest chain 19 peptides. Score 0.560 Round 4: 268 peptides, 34 chains. Longest chain 27 peptides. Score 0.553 Round 5: 259 peptides, 36 chains. Longest chain 18 peptides. Score 0.510 Taking the results from Round 3 Chains 33, Residues 230, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7297 restraints for refining 3386 atoms. 6374 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2649 (Rfree = 0.000) for 3386 atoms. Found 13 (18 requested) and removed 31 (9 requested) atoms. Cycle 17: After refmac, R = 0.2314 (Rfree = 0.000) for 3349 atoms. Found 13 (18 requested) and removed 21 (9 requested) atoms. Cycle 18: After refmac, R = 0.2248 (Rfree = 0.000) for 3334 atoms. Found 10 (18 requested) and removed 23 (9 requested) atoms. Cycle 19: After refmac, R = 0.2220 (Rfree = 0.000) for 3315 atoms. Found 8 (18 requested) and removed 19 (9 requested) atoms. Cycle 20: After refmac, R = 0.2072 (Rfree = 0.000) for 3301 atoms. Found 5 (18 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.40 Search for helices and strands: 0 residues in 0 chains, 3397 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3414 seeds are put forward Round 1: 210 peptides, 38 chains. Longest chain 13 peptides. Score 0.355 Round 2: 241 peptides, 35 chains. Longest chain 13 peptides. Score 0.476 Round 3: 258 peptides, 34 chains. Longest chain 22 peptides. Score 0.530 Round 4: 249 peptides, 30 chains. Longest chain 20 peptides. Score 0.551 Round 5: 247 peptides, 33 chains. Longest chain 22 peptides. Score 0.514 Taking the results from Round 4 Chains 30, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7480 restraints for refining 3385 atoms. 6634 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2788 (Rfree = 0.000) for 3385 atoms. Found 13 (18 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.2556 (Rfree = 0.000) for 3360 atoms. Found 16 (18 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2372 (Rfree = 0.000) for 3349 atoms. Found 15 (18 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.2136 (Rfree = 0.000) for 3335 atoms. Found 5 (18 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.2038 (Rfree = 0.000) for 3317 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 3428 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3449 seeds are put forward Round 1: 195 peptides, 38 chains. Longest chain 10 peptides. Score 0.309 Round 2: 232 peptides, 37 chains. Longest chain 12 peptides. Score 0.429 Round 3: 222 peptides, 34 chains. Longest chain 14 peptides. Score 0.438 Round 4: 239 peptides, 33 chains. Longest chain 25 peptides. Score 0.494 Round 5: 219 peptides, 35 chains. Longest chain 15 peptides. Score 0.418 Taking the results from Round 4 Chains 33, Residues 206, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7527 restraints for refining 3386 atoms. 6626 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2546 (Rfree = 0.000) for 3386 atoms. Found 15 (18 requested) and removed 27 (9 requested) atoms. Cycle 27: After refmac, R = 0.2597 (Rfree = 0.000) for 3361 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 28: After refmac, R = 0.2346 (Rfree = 0.000) for 3356 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. Cycle 29: After refmac, R = 0.2283 (Rfree = 0.000) for 3347 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2266 (Rfree = 0.000) for 3332 atoms. Found 4 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 3419 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3455 seeds are put forward Round 1: 201 peptides, 37 chains. Longest chain 14 peptides. Score 0.341 Round 2: 215 peptides, 33 chains. Longest chain 15 peptides. Score 0.431 Round 3: 209 peptides, 33 chains. Longest chain 12 peptides. Score 0.415 Round 4: 223 peptides, 31 chains. Longest chain 17 peptides. Score 0.476 Round 5: 240 peptides, 34 chains. Longest chain 18 peptides. Score 0.485 Taking the results from Round 5 Chains 34, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7795 restraints for refining 3386 atoms. 7005 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2779 (Rfree = 0.000) for 3386 atoms. Found 16 (18 requested) and removed 109 (9 requested) atoms. Cycle 32: After refmac, R = 0.2627 (Rfree = 0.000) for 3270 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 33: After refmac, R = 0.2470 (Rfree = 0.000) for 3261 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.2379 (Rfree = 0.000) for 3254 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. Cycle 35: After refmac, R = 0.2371 (Rfree = 0.000) for 3245 atoms. Found 9 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3327 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3348 seeds are put forward Round 1: 183 peptides, 37 chains. Longest chain 9 peptides. Score 0.285 Round 2: 198 peptides, 32 chains. Longest chain 14 peptides. Score 0.396 Round 3: 204 peptides, 35 chains. Longest chain 12 peptides. Score 0.375 Round 4: 207 peptides, 30 chains. Longest chain 15 peptides. Score 0.446 Round 5: 219 peptides, 32 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 5 Chains 32, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7916 restraints for refining 3386 atoms. 7200 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2691 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 37: After refmac, R = 0.2496 (Rfree = 0.000) for 3364 atoms. Found 16 (18 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.2304 (Rfree = 0.000) for 3347 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.2538 (Rfree = 0.000) for 3331 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.2409 (Rfree = 0.000) for 3327 atoms. Found 16 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 3425 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3453 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 8 peptides. Score 0.267 Round 2: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.359 Round 3: 199 peptides, 31 chains. Longest chain 19 peptides. Score 0.411 Round 4: 200 peptides, 32 chains. Longest chain 15 peptides. Score 0.402 Round 5: 201 peptides, 31 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 5 Chains 31, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7725 restraints for refining 3385 atoms. 7076 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2708 (Rfree = 0.000) for 3385 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 42: After refmac, R = 0.2387 (Rfree = 0.000) for 3363 atoms. Found 16 (18 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.2474 (Rfree = 0.000) for 3337 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.2296 (Rfree = 0.000) for 3322 atoms. Found 11 (18 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.2205 (Rfree = 0.000) for 3318 atoms. Found 6 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 3398 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3406 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 8 peptides. Score 0.231 Round 2: 156 peptides, 29 chains. Longest chain 12 peptides. Score 0.308 Round 3: 178 peptides, 31 chains. Longest chain 10 peptides. Score 0.350 Round 4: 176 peptides, 30 chains. Longest chain 11 peptides. Score 0.357 Round 5: 187 peptides, 29 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 158, 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 1z85-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6039 reflections ( 99.69 % complete ) and 7972 restraints for refining 3386 atoms. 7369 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2701 (Rfree = 0.000) for 3386 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2527 (Rfree = 0.000) for 3358 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2516 (Rfree = 0.000) for 3337 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2358 (Rfree = 0.000) for 3311 atoms. TimeTaking 38.27