Sun 23 Dec 22:22:52 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 2h1q-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-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/2h1q-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-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 22:23:02 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/2h1q-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-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 384 and 0 Target number of residues in the AU: 384 Target solvent content: 0.6717 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.54 Input MTZ file: 2h1q-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4320 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: 28.996 3.801 Wilson plot Bfac: 93.94 6233 reflections ( 99.58 % complete ) and 0 restraints for refining 4781 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3457 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 4781 atoms. Found 26 (26 requested) and removed 66 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 3.61 Search for helices and strands: 0 residues in 0 chains, 4808 seeds are put forward NCS extension: 0 residues added, 4808 seeds are put forward Round 1: 136 peptides, 28 chains. Longest chain 8 peptides. Score 0.250 Round 2: 188 peptides, 38 chains. Longest chain 10 peptides. Score 0.280 Round 3: 212 peptides, 36 chains. Longest chain 10 peptides. Score 0.371 Round 4: 219 peptides, 34 chains. Longest chain 14 peptides. Score 0.413 Round 5: 227 peptides, 38 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 4 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 9423 restraints for refining 3808 atoms. 8702 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2950 (Rfree = 0.000) for 3808 atoms. Found 20 (20 requested) and removed 45 (10 requested) atoms. Cycle 2: After refmac, R = 0.2981 (Rfree = 0.000) for 3682 atoms. Found 20 (20 requested) and removed 37 (10 requested) atoms. Cycle 3: After refmac, R = 0.2487 (Rfree = 0.000) for 3608 atoms. Found 9 (20 requested) and removed 35 (10 requested) atoms. Cycle 4: After refmac, R = 0.2901 (Rfree = 0.000) for 3545 atoms. Found 19 (19 requested) and removed 36 (9 requested) atoms. Cycle 5: After refmac, R = 0.2723 (Rfree = 0.000) for 3490 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 3580 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3596 seeds are put forward Round 1: 167 peptides, 34 chains. Longest chain 8 peptides. Score 0.268 Round 2: 220 peptides, 38 chains. Longest chain 10 peptides. Score 0.369 Round 3: 237 peptides, 40 chains. Longest chain 11 peptides. Score 0.391 Round 4: 251 peptides, 41 chains. Longest chain 12 peptides. Score 0.416 Round 5: 236 peptides, 34 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Chains 34, Residues 202, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 7822 restraints for refining 3400 atoms. 7007 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2758 (Rfree = 0.000) for 3400 atoms. Found 18 (18 requested) and removed 50 (9 requested) atoms. Cycle 7: After refmac, R = 0.2678 (Rfree = 0.000) for 3336 atoms. Found 18 (18 requested) and removed 46 (9 requested) atoms. Cycle 8: After refmac, R = 0.2608 (Rfree = 0.000) for 3285 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 9: After refmac, R = 0.2823 (Rfree = 0.000) for 3263 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 10: After refmac, R = 0.2593 (Rfree = 0.000) for 3218 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3388 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3403 seeds are put forward Round 1: 200 peptides, 41 chains. Longest chain 9 peptides. Score 0.278 Round 2: 230 peptides, 40 chains. Longest chain 11 peptides. Score 0.373 Round 3: 258 peptides, 43 chains. Longest chain 14 peptides. Score 0.412 Round 4: 268 peptides, 43 chains. Longest chain 13 peptides. Score 0.436 Round 5: 269 peptides, 42 chains. Longest chain 13 peptides. Score 0.449 Taking the results from Round 5 Chains 42, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 7740 restraints for refining 3471 atoms. 6874 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2747 (Rfree = 0.000) for 3471 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 12: After refmac, R = 0.2604 (Rfree = 0.000) for 3407 atoms. Found 18 (18 requested) and removed 48 (9 requested) atoms. Cycle 13: After refmac, R = 0.2574 (Rfree = 0.000) for 3349 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 14: After refmac, R = 0.2339 (Rfree = 0.000) for 3320 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.2389 (Rfree = 0.000) for 3299 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.58 Search for helices and strands: 0 residues in 0 chains, 3475 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3489 seeds are put forward Round 1: 200 peptides, 43 chains. Longest chain 8 peptides. Score 0.253 Round 2: 240 peptides, 43 chains. Longest chain 12 peptides. Score 0.365 Round 3: 245 peptides, 38 chains. Longest chain 12 peptides. Score 0.434 Round 4: 250 peptides, 41 chains. Longest chain 11 peptides. Score 0.413 Round 5: 251 peptides, 37 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 5 Chains 37, Residues 214, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 7596 restraints for refining 3534 atoms. 6656 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2670 (Rfree = 0.000) for 3534 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 17: After refmac, R = 0.2511 (Rfree = 0.000) for 3473 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 18: After refmac, R = 0.2417 (Rfree = 0.000) for 3433 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 19: After refmac, R = 0.1972 (Rfree = 0.000) for 3404 atoms. Found 10 (18 requested) and removed 15 (9 requested) atoms. Cycle 20: After refmac, R = 0.1836 (Rfree = 0.000) for 3394 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3548 seeds are put forward Round 1: 215 peptides, 43 chains. Longest chain 12 peptides. Score 0.297 Round 2: 249 peptides, 44 chains. Longest chain 13 peptides. Score 0.377 Round 3: 242 peptides, 42 chains. Longest chain 13 peptides. Score 0.382 Round 4: 246 peptides, 42 chains. Longest chain 14 peptides. Score 0.392 Round 5: 241 peptides, 39 chains. Longest chain 16 peptides. Score 0.413 Taking the results from Round 5 Chains 39, Residues 202, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8331 restraints for refining 3615 atoms. 7550 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2684 (Rfree = 0.000) for 3615 atoms. Found 19 (19 requested) and removed 47 (9 requested) atoms. Cycle 22: After refmac, R = 0.2458 (Rfree = 0.000) for 3553 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 23: After refmac, R = 0.2522 (Rfree = 0.000) for 3520 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 24: After refmac, R = 0.2509 (Rfree = 0.000) for 3488 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 25: After refmac, R = 0.2460 (Rfree = 0.000) for 3461 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 3602 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3624 seeds are put forward Round 1: 179 peptides, 36 chains. Longest chain 10 peptides. Score 0.278 Round 2: 216 peptides, 38 chains. Longest chain 10 peptides. Score 0.359 Round 3: 192 peptides, 34 chains. Longest chain 10 peptides. Score 0.341 Round 4: 202 peptides, 34 chains. Longest chain 9 peptides. Score 0.368 Round 5: 221 peptides, 35 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Chains 35, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8012 restraints for refining 3497 atoms. 7303 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2561 (Rfree = 0.000) for 3497 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 27: After refmac, R = 0.2440 (Rfree = 0.000) for 3448 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 28: After refmac, R = 0.2455 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 29: After refmac, R = 0.2441 (Rfree = 0.000) for 3391 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 30: After refmac, R = 0.2449 (Rfree = 0.000) for 3379 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 0 residues added, 3501 seeds are put forward Round 1: 179 peptides, 38 chains. Longest chain 10 peptides. Score 0.253 Round 2: 203 peptides, 38 chains. Longest chain 10 peptides. Score 0.323 Round 3: 208 peptides, 38 chains. Longest chain 9 peptides. Score 0.337 Round 4: 222 peptides, 41 chains. Longest chain 10 peptides. Score 0.340 Round 5: 229 peptides, 38 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 5 Chains 38, Residues 191, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 7976 restraints for refining 3541 atoms. 7224 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2516 (Rfree = 0.000) for 3541 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 32: After refmac, R = 0.2375 (Rfree = 0.000) for 3502 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 33: After refmac, R = 0.2263 (Rfree = 0.000) for 3465 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 34: After refmac, R = 0.1875 (Rfree = 0.000) for 3451 atoms. Found 7 (19 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.2256 (Rfree = 0.000) for 3427 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.57 Search for helices and strands: 0 residues in 0 chains, 3546 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3558 seeds are put forward Round 1: 147 peptides, 30 chains. Longest chain 8 peptides. Score 0.258 Round 2: 177 peptides, 31 chains. Longest chain 9 peptides. Score 0.335 Round 3: 181 peptides, 32 chains. Longest chain 15 peptides. Score 0.334 Round 4: 183 peptides, 32 chains. Longest chain 10 peptides. Score 0.340 Round 5: 183 peptides, 31 chains. Longest chain 11 peptides. Score 0.352 Taking the results from Round 5 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8360 restraints for refining 3546 atoms. 7783 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2535 (Rfree = 0.000) for 3546 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 37: After refmac, R = 0.2557 (Rfree = 0.000) for 3518 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 38: After refmac, R = 0.2483 (Rfree = 0.000) for 3489 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 39: After refmac, R = 0.2490 (Rfree = 0.000) for 3467 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 40: After refmac, R = 0.2540 (Rfree = 0.000) for 3457 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.57 Search for helices and strands: 0 residues in 0 chains, 3545 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3558 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 11 peptides. Score 0.249 Round 2: 153 peptides, 31 chains. Longest chain 8 peptides. Score 0.264 Round 3: 165 peptides, 32 chains. Longest chain 10 peptides. Score 0.287 Round 4: 175 peptides, 31 chains. Longest chain 14 peptides. Score 0.330 Round 5: 169 peptides, 32 chains. Longest chain 11 peptides. Score 0.299 Taking the results from Round 4 Chains 31, Residues 144, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 7426 restraints for refining 3333 atoms. 6854 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2395 (Rfree = 0.000) for 3333 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 42: After refmac, R = 0.2490 (Rfree = 0.000) for 3316 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 43: After refmac, R = 0.2226 (Rfree = 0.000) for 3296 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.2565 (Rfree = 0.000) for 3290 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 45: After refmac, R = 0.2275 (Rfree = 0.000) for 3287 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 3409 seeds are put forward NCS extension: 0 residues added, 3409 seeds are put forward Round 1: 144 peptides, 31 chains. Longest chain 10 peptides. Score 0.235 Round 2: 197 peptides, 38 chains. Longest chain 12 peptides. Score 0.306 Round 3: 193 peptides, 38 chains. Longest chain 10 peptides. Score 0.294 Round 4: 190 peptides, 37 chains. Longest chain 11 peptides. Score 0.298 Round 5: 188 peptides, 34 chains. Longest chain 10 peptides. Score 0.329 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 154, 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 2h1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6233 reflections ( 99.58 % complete ) and 7391 restraints for refining 3340 atoms. 6809 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2477 (Rfree = 0.000) for 3340 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2364 (Rfree = 0.000) for 3317 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2614 (Rfree = 0.000) for 3294 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2501 (Rfree = 0.000) for 3270 atoms. TimeTaking 58.28