Tue 25 Dec 19:27:57 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 2fg0-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-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/2fg0-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-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 ============================================================ Tue 25 Dec 19:28:06 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/2fg0-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6592 Checking the provided sequence file Detected sequence length: 246 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 492 Adjusted target solvent content: 0.65 Input MTZ file: 2fg0-4.0-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3936 target number of atoms Had to go as low as 0.80 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: 88.311 4.000 Wilson plot Bfac: 84.34 6886 reflections ( 99.59 % complete ) and 0 restraints for refining 4357 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3128 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3173 (Rfree = 0.000) for 4357 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.05 Search for helices and strands: 0 residues in 0 chains, 4427 seeds are put forward NCS extension: 0 residues added, 4427 seeds are put forward Round 1: 238 peptides, 40 chains. Longest chain 12 peptides. Score 0.366 Round 2: 265 peptides, 32 chains. Longest chain 24 peptides. Score 0.499 Round 3: 298 peptides, 30 chains. Longest chain 24 peptides. Score 0.576 Round 4: 304 peptides, 27 chains. Longest chain 34 peptides. Score 0.610 Round 5: 295 peptides, 27 chains. Longest chain 30 peptides. Score 0.595 Taking the results from Round 4 Chains 31, Residues 277, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7705 restraints for refining 3554 atoms. 6519 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2508 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 2: After refmac, R = 0.2307 (Rfree = 0.000) for 3478 atoms. Found 10 (16 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2288 (Rfree = 0.000) for 3442 atoms. Found 11 (16 requested) and removed 18 (8 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 3400 atoms. Found 14 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2275 (Rfree = 0.000) for 3379 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3499 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3521 seeds are put forward Round 1: 278 peptides, 38 chains. Longest chain 16 peptides. Score 0.470 Round 2: 303 peptides, 28 chains. Longest chain 41 peptides. Score 0.601 Round 3: 291 peptides, 29 chains. Longest chain 21 peptides. Score 0.572 Round 4: 307 peptides, 28 chains. Longest chain 41 peptides. Score 0.607 Round 5: 304 peptides, 31 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 4 Chains 34, Residues 279, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6886 reflections ( 99.59 % complete ) and 7403 restraints for refining 3554 atoms. 6152 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2476 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 45 (8 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2368 (Rfree = 0.000) for 3476 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2284 (Rfree = 0.000) for 3449 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.2283 (Rfree = 0.000) for 3421 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2199 (Rfree = 0.000) for 3404 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.02 Search for helices and strands: 0 residues in 0 chains, 3538 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3557 seeds are put forward Round 1: 292 peptides, 33 chains. Longest chain 27 peptides. Score 0.541 Round 2: 294 peptides, 32 chains. Longest chain 19 peptides. Score 0.553 Round 3: 306 peptides, 33 chains. Longest chain 24 peptides. Score 0.565 Round 4: 299 peptides, 29 chains. Longest chain 22 peptides. Score 0.586 Round 5: 317 peptides, 29 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 5 Chains 29, Residues 288, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7918 restraints for refining 3551 atoms. 6795 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2664 (Rfree = 0.000) for 3551 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2452 (Rfree = 0.000) for 3495 atoms. Found 15 (16 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.2337 (Rfree = 0.000) for 3454 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2138 (Rfree = 0.000) for 3428 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2072 (Rfree = 0.000) for 3410 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3500 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3523 seeds are put forward Round 1: 279 peptides, 40 chains. Longest chain 18 peptides. Score 0.454 Round 2: 290 peptides, 30 chains. Longest chain 26 peptides. Score 0.562 Round 3: 306 peptides, 37 chains. Longest chain 25 peptides. Score 0.532 Round 4: 303 peptides, 37 chains. Longest chain 22 peptides. Score 0.527 Round 5: 311 peptides, 33 chains. Longest chain 22 peptides. Score 0.574 Taking the results from Round 5 Chains 33, Residues 278, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6886 reflections ( 99.59 % complete ) and 7875 restraints for refining 3555 atoms. 6776 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2580 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2491 (Rfree = 0.000) for 3522 atoms. Found 10 (16 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.2750 (Rfree = 0.000) for 3503 atoms. Found 12 (16 requested) and removed 28 (8 requested) atoms. Cycle 19: After refmac, R = 0.2758 (Rfree = 0.000) for 3480 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2651 (Rfree = 0.000) for 3474 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.11 Search for helices and strands: 0 residues in 0 chains, 3566 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3583 seeds are put forward Round 1: 267 peptides, 36 chains. Longest chain 14 peptides. Score 0.466 Round 2: 280 peptides, 28 chains. Longest chain 31 peptides. Score 0.562 Round 3: 282 peptides, 32 chains. Longest chain 23 peptides. Score 0.531 Round 4: 286 peptides, 35 chains. Longest chain 23 peptides. Score 0.512 Round 5: 287 peptides, 29 chains. Longest chain 26 peptides. Score 0.565 Taking the results from Round 5 Chains 31, Residues 258, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7903 restraints for refining 3554 atoms. 6842 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2920 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.2702 (Rfree = 0.000) for 3519 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.2578 (Rfree = 0.000) for 3493 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 24: After refmac, R = 0.2393 (Rfree = 0.000) for 3470 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.2758 (Rfree = 0.000) for 3463 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.04 Search for helices and strands: 0 residues in 0 chains, 3579 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3600 seeds are put forward Round 1: 244 peptides, 44 chains. Longest chain 15 peptides. Score 0.340 Round 2: 268 peptides, 35 chains. Longest chain 20 peptides. Score 0.478 Round 3: 289 peptides, 38 chains. Longest chain 22 peptides. Score 0.492 Round 4: 285 peptides, 35 chains. Longest chain 29 peptides. Score 0.511 Round 5: 299 peptides, 29 chains. Longest chain 36 peptides. Score 0.586 Taking the results from Round 5 Chains 34, Residues 270, Estimated correctness of the model 0.0 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7383 restraints for refining 3555 atoms. 6132 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2797 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2854 (Rfree = 0.000) for 3516 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 28: After refmac, R = 0.2861 (Rfree = 0.000) for 3492 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 29: After refmac, R = 0.2493 (Rfree = 0.000) for 3466 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 30: After refmac, R = 0.2183 (Rfree = 0.000) for 3425 atoms. Found 4 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3523 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3540 seeds are put forward Round 1: 256 peptides, 44 chains. Longest chain 13 peptides. Score 0.367 Round 2: 260 peptides, 34 chains. Longest chain 20 peptides. Score 0.471 Round 3: 275 peptides, 37 chains. Longest chain 16 peptides. Score 0.473 Round 4: 266 peptides, 36 chains. Longest chain 17 peptides. Score 0.464 Round 5: 274 peptides, 35 chains. Longest chain 19 peptides. Score 0.489 Taking the results from Round 5 Chains 36, Residues 239, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7957 restraints for refining 3554 atoms. 6933 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2609 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2612 (Rfree = 0.000) for 3494 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 33: After refmac, R = 0.2525 (Rfree = 0.000) for 3447 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.2389 (Rfree = 0.000) for 3402 atoms. Found 9 (16 requested) and removed 27 (8 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2335 (Rfree = 0.000) for 3360 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 3477 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3499 seeds are put forward Round 1: 238 peptides, 45 chains. Longest chain 13 peptides. Score 0.316 Round 2: 278 peptides, 41 chains. Longest chain 20 peptides. Score 0.443 Round 3: 287 peptides, 39 chains. Longest chain 29 peptides. Score 0.479 Round 4: 286 peptides, 37 chains. Longest chain 21 peptides. Score 0.495 Round 5: 269 peptides, 37 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 4 Chains 39, Residues 249, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6886 reflections ( 99.59 % complete ) and 7691 restraints for refining 3555 atoms. 6600 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2938 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 37: After refmac, R = 0.3107 (Rfree = 0.000) for 3521 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 38: After refmac, R = 0.2419 (Rfree = 0.000) for 3495 atoms. Found 15 (16 requested) and removed 25 (8 requested) atoms. Cycle 39: After refmac, R = 0.2842 (Rfree = 0.000) for 3482 atoms. Found 12 (16 requested) and removed 38 (8 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2780 (Rfree = 0.000) for 3449 atoms. Found 15 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.02 Search for helices and strands: 0 residues in 0 chains, 3556 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3582 seeds are put forward Round 1: 221 peptides, 37 chains. Longest chain 16 peptides. Score 0.357 Round 2: 260 peptides, 34 chains. Longest chain 21 peptides. Score 0.471 Round 3: 258 peptides, 36 chains. Longest chain 24 peptides. Score 0.448 Round 4: 269 peptides, 38 chains. Longest chain 18 peptides. Score 0.452 Round 5: 251 peptides, 33 chains. Longest chain 14 peptides. Score 0.462 Taking the results from Round 2 Chains 38, Residues 226, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7926 restraints for refining 3554 atoms. 6965 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2432 (Rfree = 0.000) for 3554 atoms. Found 13 (16 requested) and removed 20 (8 requested) atoms. Cycle 42: After refmac, R = 0.2307 (Rfree = 0.000) for 3506 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 43: After refmac, R = 0.2186 (Rfree = 0.000) for 3488 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.2124 (Rfree = 0.000) for 3471 atoms. Found 9 (16 requested) and removed 14 (8 requested) atoms. Cycle 45: After refmac, R = 0.2069 (Rfree = 0.000) for 3460 atoms. Found 10 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3543 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 3576 seeds are put forward Round 1: 231 peptides, 41 chains. Longest chain 17 peptides. Score 0.340 Round 2: 250 peptides, 39 chains. Longest chain 19 peptides. Score 0.403 Round 3: 234 peptides, 35 chains. Longest chain 22 peptides. Score 0.407 Round 4: 252 peptides, 35 chains. Longest chain 15 peptides. Score 0.445 Round 5: 239 peptides, 37 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 217, 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 2fg0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6886 reflections ( 99.59 % complete ) and 8208 restraints for refining 3555 atoms. 7375 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2485 (Rfree = 0.000) for 3555 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2496 (Rfree = 0.000) for 3496 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2411 (Rfree = 0.000) for 3469 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2376 (Rfree = 0.000) for 3444 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 64.63