null Sun 23 Dec 22:22:41 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 1z85-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z85-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.8-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/1z85-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.8-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 22:22:50 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/1z85-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-3.8-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 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-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: 19 Cell parameters: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3744 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: 65.199 3.800 Wilson plot Bfac: 81.51 6039 reflections ( 99.69 % complete ) and 0 restraints for refining 4138 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3359 (Rfree = 0.000) for 4138 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.48 Search for helices and strands: 0 residues in 0 chains, 4202 seeds are put forward NCS extension: 0 residues added, 4202 seeds are put forward Round 1: 181 peptides, 29 chains. Longest chain 11 peptides. Score 0.385 Round 2: 242 peptides, 33 chains. Longest chain 28 peptides. Score 0.502 Round 3: 266 peptides, 32 chains. Longest chain 26 peptides. Score 0.569 Round 4: 272 peptides, 32 chains. Longest chain 28 peptides. Score 0.582 Round 5: 276 peptides, 26 chains. Longest chain 30 peptides. Score 0.648 Taking the results from Round 5 Chains 30, Residues 250, Estimated correctness of the model 20.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7309 restraints for refining 3383 atoms. 6220 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 3383 atoms. Found 10 (18 requested) and removed 29 (9 requested) atoms. Cycle 2: After refmac, R = 0.2973 (Rfree = 0.000) for 3276 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 3: After refmac, R = 0.2810 (Rfree = 0.000) for 3231 atoms. Found 10 (17 requested) and removed 19 (8 requested) atoms. Cycle 4: After refmac, R = 0.2861 (Rfree = 0.000) for 3174 atoms. Found 16 (17 requested) and removed 31 (8 requested) atoms. Cycle 5: After refmac, R = 0.2744 (Rfree = 0.000) for 3131 atoms. Found 9 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 3237 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3251 seeds are put forward Round 1: 237 peptides, 40 chains. Longest chain 13 peptides. Score 0.407 Round 2: 267 peptides, 38 chains. Longest chain 16 peptides. Score 0.508 Round 3: 272 peptides, 37 chains. Longest chain 16 peptides. Score 0.531 Round 4: 278 peptides, 37 chains. Longest chain 15 peptides. Score 0.545 Round 5: 282 peptides, 35 chains. Longest chain 19 peptides. Score 0.574 Taking the results from Round 5 Chains 35, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7595 restraints for refining 3359 atoms. 6642 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2815 (Rfree = 0.000) for 3359 atoms. Found 10 (18 requested) and removed 27 (9 requested) atoms. Cycle 7: After refmac, R = 0.2634 (Rfree = 0.000) for 3297 atoms. Found 11 (18 requested) and removed 24 (9 requested) atoms. Cycle 8: After refmac, R = 0.2571 (Rfree = 0.000) for 3251 atoms. Found 12 (18 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.2466 (Rfree = 0.000) for 3217 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2289 (Rfree = 0.000) for 3187 atoms. Found 4 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.42 Search for helices and strands: 0 residues in 0 chains, 3290 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3318 seeds are put forward Round 1: 268 peptides, 46 chains. Longest chain 13 peptides. Score 0.421 Round 2: 285 peptides, 38 chains. Longest chain 23 peptides. Score 0.551 Round 3: 276 peptides, 37 chains. Longest chain 25 peptides. Score 0.540 Round 4: 274 peptides, 39 chains. Longest chain 19 peptides. Score 0.514 Round 5: 272 peptides, 37 chains. Longest chain 18 peptides. Score 0.531 Taking the results from Round 2 Chains 40, Residues 247, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 6918 restraints for refining 3286 atoms. 5870 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2521 (Rfree = 0.000) for 3286 atoms. Found 7 (18 requested) and removed 26 (9 requested) atoms. Cycle 12: After refmac, R = 0.2428 (Rfree = 0.000) for 3233 atoms. Found 13 (17 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.2347 (Rfree = 0.000) for 3224 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2359 (Rfree = 0.000) for 3205 atoms. Found 14 (17 requested) and removed 20 (8 requested) atoms. Cycle 15: After refmac, R = 0.2479 (Rfree = 0.000) for 3186 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 3298 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 3330 seeds are put forward Round 1: 224 peptides, 38 chains. Longest chain 14 peptides. Score 0.395 Round 2: 249 peptides, 34 chains. Longest chain 15 peptides. Score 0.508 Round 3: 259 peptides, 32 chains. Longest chain 25 peptides. Score 0.553 Round 4: 254 peptides, 33 chains. Longest chain 20 peptides. Score 0.531 Round 5: 257 peptides, 34 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 3 Chains 34, Residues 227, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7487 restraints for refining 3386 atoms. 6549 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2886 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 58 (9 requested) atoms. Cycle 17: After refmac, R = 0.2528 (Rfree = 0.000) for 3314 atoms. Found 7 (18 requested) and removed 29 (9 requested) atoms. Cycle 18: After refmac, R = 0.2427 (Rfree = 0.000) for 3273 atoms. Found 11 (18 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.2338 (Rfree = 0.000) for 3260 atoms. Found 5 (17 requested) and removed 19 (8 requested) atoms. Cycle 20: After refmac, R = 0.2406 (Rfree = 0.000) for 3235 atoms. Found 7 (17 requested) and removed 35 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.40 Search for helices and strands: 0 residues in 0 chains, 3279 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3303 seeds are put forward Round 1: 212 peptides, 42 chains. Longest chain 9 peptides. Score 0.310 Round 2: 236 peptides, 40 chains. Longest chain 13 peptides. Score 0.404 Round 3: 236 peptides, 34 chains. Longest chain 17 peptides. Score 0.475 Round 4: 248 peptides, 38 chains. Longest chain 17 peptides. Score 0.460 Round 5: 244 peptides, 37 chains. Longest chain 18 peptides. Score 0.461 Taking the results from Round 3 Chains 34, Residues 202, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7314 restraints for refining 3321 atoms. 6525 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2641 (Rfree = 0.000) for 3321 atoms. Found 13 (18 requested) and removed 30 (9 requested) atoms. Cycle 22: After refmac, R = 0.2602 (Rfree = 0.000) for 3288 atoms. Found 17 (18 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.2641 (Rfree = 0.000) for 3276 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 24: After refmac, R = 0.2627 (Rfree = 0.000) for 3261 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 25: After refmac, R = 0.2653 (Rfree = 0.000) for 3250 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 3356 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3368 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 10 peptides. Score 0.294 Round 2: 244 peptides, 42 chains. Longest chain 18 peptides. Score 0.403 Round 3: 214 peptides, 35 chains. Longest chain 13 peptides. Score 0.404 Round 4: 219 peptides, 36 chains. Longest chain 13 peptides. Score 0.406 Round 5: 227 peptides, 35 chains. Longest chain 23 peptides. Score 0.440 Taking the results from Round 5 Chains 35, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7881 restraints for refining 3383 atoms. 7148 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2608 (Rfree = 0.000) for 3383 atoms. Found 8 (18 requested) and removed 19 (9 requested) atoms. Cycle 27: After refmac, R = 0.2544 (Rfree = 0.000) for 3346 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 28: After refmac, R = 0.2660 (Rfree = 0.000) for 3320 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 29: After refmac, R = 0.2545 (Rfree = 0.000) for 3302 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.2595 (Rfree = 0.000) for 3300 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3403 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3427 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 9 peptides. Score 0.273 Round 2: 214 peptides, 35 chains. Longest chain 14 peptides. Score 0.404 Round 3: 208 peptides, 34 chains. Longest chain 12 peptides. Score 0.399 Round 4: 231 peptides, 33 chains. Longest chain 18 peptides. Score 0.474 Round 5: 221 peptides, 35 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 4 Chains 33, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7686 restraints for refining 3386 atoms. 6927 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2712 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 32: After refmac, R = 0.2717 (Rfree = 0.000) for 3354 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.2949 (Rfree = 0.000) for 3324 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 34: After refmac, R = 0.2731 (Rfree = 0.000) for 3297 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 35: After refmac, R = 0.2774 (Rfree = 0.000) for 3285 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.46 Search for helices and strands: 0 residues in 0 chains, 3369 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3383 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 8 peptides. Score 0.278 Round 2: 200 peptides, 36 chains. Longest chain 9 peptides. Score 0.351 Round 3: 207 peptides, 36 chains. Longest chain 10 peptides. Score 0.371 Round 4: 229 peptides, 35 chains. Longest chain 16 peptides. Score 0.445 Round 5: 238 peptides, 34 chains. Longest chain 16 peptides. Score 0.480 Taking the results from Round 5 Chains 34, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7513 restraints for refining 3358 atoms. 6731 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2702 (Rfree = 0.000) for 3358 atoms. Found 11 (18 requested) and removed 30 (9 requested) atoms. Cycle 37: After refmac, R = 0.2476 (Rfree = 0.000) for 3316 atoms. Found 7 (18 requested) and removed 21 (9 requested) atoms. Cycle 38: After refmac, R = 0.2544 (Rfree = 0.000) for 3291 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.2490 (Rfree = 0.000) for 3264 atoms. Found 9 (18 requested) and removed 13 (9 requested) atoms. Cycle 40: After refmac, R = 0.2660 (Rfree = 0.000) for 3246 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3341 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3355 seeds are put forward Round 1: 168 peptides, 35 chains. Longest chain 11 peptides. Score 0.264 Round 2: 179 peptides, 31 chains. Longest chain 10 peptides. Score 0.353 Round 3: 196 peptides, 33 chains. Longest chain 12 peptides. Score 0.377 Round 4: 202 peptides, 30 chains. Longest chain 16 peptides. Score 0.432 Round 5: 201 peptides, 30 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 4 Chains 30, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6039 reflections ( 99.69 % complete ) and 7940 restraints for refining 3380 atoms. 7282 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2862 (Rfree = 0.000) for 3380 atoms. Found 18 (18 requested) and removed 81 (9 requested) atoms. Cycle 42: After refmac, R = 0.2747 (Rfree = 0.000) for 3299 atoms. Found 17 (18 requested) and removed 39 (9 requested) atoms. Cycle 43: After refmac, R = 0.2703 (Rfree = 0.000) for 3266 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 44: After refmac, R = 0.2690 (Rfree = 0.000) for 3243 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 45: After refmac, R = 0.2647 (Rfree = 0.000) for 3214 atoms. Found 14 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 3265 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3283 seeds are put forward Round 1: 142 peptides, 32 chains. Longest chain 8 peptides. Score 0.218 Round 2: 159 peptides, 33 chains. Longest chain 8 peptides. Score 0.262 Round 3: 156 peptides, 31 chains. Longest chain 8 peptides. Score 0.280 Round 4: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.309 Round 5: 148 peptides, 28 chains. Longest chain 10 peptides. Score 0.296 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 124, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1z85-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (124 residues) following loop building 3 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6039 reflections ( 99.69 % complete ) and 7461 restraints for refining 3238 atoms. 6954 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2854 (Rfree = 0.000) for 3238 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2860 (Rfree = 0.000) for 3212 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2573 (Rfree = 0.000) for 3185 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2630 (Rfree = 0.000) for 3167 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:58 GMT 2018 Job finished. TimeTaking 55.28 Used memory is bytes: 4575448