null Mon 24 Dec 00:26:30 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 2h1q-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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/2h1q-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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 ============================================================ Mon 24 Dec 00:26:34 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/2h1q-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-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 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-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-3.8-parrot-mrncs.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 4756 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3422 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3352 (Rfree = 0.000) for 4756 atoms. Found 26 (26 requested) and removed 44 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.59 Search for helices and strands: 0 residues in 0 chains, 4812 seeds are put forward NCS extension: 0 residues added, 4812 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 8 peptides. Score 0.241 Round 2: 186 peptides, 37 chains. Longest chain 13 peptides. Score 0.286 Round 3: 218 peptides, 37 chains. Longest chain 17 peptides. Score 0.376 Round 4: 233 peptides, 36 chains. Longest chain 15 peptides. Score 0.426 Round 5: 247 peptides, 40 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 4 Chains 36, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 9128 restraints for refining 3758 atoms. 8376 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2958 (Rfree = 0.000) for 3758 atoms. Found 20 (20 requested) and removed 61 (10 requested) atoms. Cycle 2: After refmac, R = 0.2739 (Rfree = 0.000) for 3647 atoms. Found 20 (20 requested) and removed 43 (10 requested) atoms. Cycle 3: After refmac, R = 0.2723 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 44 (9 requested) atoms. Cycle 4: After refmac, R = 0.2606 (Rfree = 0.000) for 3509 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 5: After refmac, R = 0.2593 (Rfree = 0.000) for 3477 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 3588 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3609 seeds are put forward Round 1: 204 peptides, 43 chains. Longest chain 9 peptides. Score 0.265 Round 2: 227 peptides, 41 chains. Longest chain 17 peptides. Score 0.353 Round 3: 229 peptides, 40 chains. Longest chain 11 peptides. Score 0.370 Round 4: 244 peptides, 42 chains. Longest chain 15 peptides. Score 0.387 Round 5: 246 peptides, 39 chains. Longest chain 16 peptides. Score 0.425 Taking the results from Round 5 Chains 39, Residues 207, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8106 restraints for refining 3464 atoms. 7311 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2596 (Rfree = 0.000) for 3464 atoms. Found 19 (19 requested) and removed 45 (9 requested) atoms. Cycle 7: After refmac, R = 0.2450 (Rfree = 0.000) for 3378 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 8: After refmac, R = 0.2267 (Rfree = 0.000) for 3322 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 3305 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 10: After refmac, R = 0.2311 (Rfree = 0.000) for 3293 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3444 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3458 seeds are put forward Round 1: 224 peptides, 43 chains. Longest chain 11 peptides. Score 0.322 Round 2: 237 peptides, 41 chains. Longest chain 10 peptides. Score 0.380 Round 3: 261 peptides, 39 chains. Longest chain 19 peptides. Score 0.462 Round 4: 273 peptides, 42 chains. Longest chain 21 peptides. Score 0.459 Round 5: 254 peptides, 33 chains. Longest chain 33 peptides. Score 0.508 Taking the results from Round 5 Chains 34, Residues 221, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8110 restraints for refining 3606 atoms. 7187 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2723 (Rfree = 0.000) for 3606 atoms. Found 19 (19 requested) and removed 56 (9 requested) atoms. Cycle 12: After refmac, R = 0.2470 (Rfree = 0.000) for 3538 atoms. Found 19 (19 requested) and removed 38 (9 requested) atoms. Cycle 13: After refmac, R = 0.2432 (Rfree = 0.000) for 3497 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 14: After refmac, R = 0.2469 (Rfree = 0.000) for 3462 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 15: After refmac, R = 0.2360 (Rfree = 0.000) for 3442 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3612 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3635 seeds are put forward Round 1: 205 peptides, 41 chains. Longest chain 12 peptides. Score 0.292 Round 2: 236 peptides, 40 chains. Longest chain 16 peptides. Score 0.389 Round 3: 232 peptides, 37 chains. Longest chain 17 peptides. Score 0.412 Round 4: 248 peptides, 37 chains. Longest chain 14 peptides. Score 0.452 Round 5: 237 peptides, 39 chains. Longest chain 15 peptides. Score 0.403 Taking the results from Round 4 Chains 37, Residues 211, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8160 restraints for refining 3523 atoms. 7337 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2632 (Rfree = 0.000) for 3523 atoms. Found 19 (19 requested) and removed 36 (9 requested) atoms. Cycle 17: After refmac, R = 0.2605 (Rfree = 0.000) for 3471 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 18: After refmac, R = 0.2484 (Rfree = 0.000) for 3437 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 19: After refmac, R = 0.2383 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 20: After refmac, R = 0.2288 (Rfree = 0.000) for 3395 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3563 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3579 seeds are put forward Round 1: 190 peptides, 41 chains. Longest chain 7 peptides. Score 0.248 Round 2: 226 peptides, 44 chains. Longest chain 10 peptides. Score 0.316 Round 3: 240 peptides, 40 chains. Longest chain 13 peptides. Score 0.399 Round 4: 240 peptides, 38 chains. Longest chain 11 peptides. Score 0.421 Round 5: 227 peptides, 36 chains. Longest chain 14 peptides. Score 0.411 Taking the results from Round 4 Chains 39, Residues 202, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8067 restraints for refining 3580 atoms. 7259 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2461 (Rfree = 0.000) for 3580 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. Cycle 22: After refmac, R = 0.2321 (Rfree = 0.000) for 3522 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 23: After refmac, R = 0.2312 (Rfree = 0.000) for 3506 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 24: After refmac, R = 0.2154 (Rfree = 0.000) for 3484 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.2148 (Rfree = 0.000) for 3473 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.58 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3598 seeds are put forward Round 1: 184 peptides, 32 chains. Longest chain 14 peptides. Score 0.343 Round 2: 213 peptides, 34 chains. Longest chain 15 peptides. Score 0.397 Round 3: 222 peptides, 34 chains. Longest chain 18 peptides. Score 0.421 Round 4: 229 peptides, 33 chains. Longest chain 16 peptides. Score 0.449 Round 5: 230 peptides, 35 chains. Longest chain 17 peptides. Score 0.429 Taking the results from Round 4 Chains 33, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8059 restraints for refining 3560 atoms. 7308 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 3560 atoms. Found 15 (19 requested) and removed 39 (9 requested) atoms. Cycle 27: After refmac, R = 0.2287 (Rfree = 0.000) for 3521 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 28: After refmac, R = 0.2286 (Rfree = 0.000) for 3499 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 29: After refmac, R = 0.2063 (Rfree = 0.000) for 3483 atoms. Found 9 (19 requested) and removed 18 (9 requested) atoms. Cycle 30: After refmac, R = 0.2235 (Rfree = 0.000) for 3468 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3612 seeds are put forward Round 1: 187 peptides, 38 chains. Longest chain 12 peptides. Score 0.277 Round 2: 225 peptides, 34 chains. Longest chain 13 peptides. Score 0.428 Round 3: 222 peptides, 35 chains. Longest chain 13 peptides. Score 0.409 Round 4: 231 peptides, 37 chains. Longest chain 18 peptides. Score 0.410 Round 5: 228 peptides, 35 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 2 Chains 34, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8142 restraints for refining 3596 atoms. 7412 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2144 (Rfree = 0.000) for 3596 atoms. Found 15 (19 requested) and removed 31 (9 requested) atoms. Cycle 32: After refmac, R = 0.2246 (Rfree = 0.000) for 3554 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 33: After refmac, R = 0.2125 (Rfree = 0.000) for 3526 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 34: After refmac, R = 0.1828 (Rfree = 0.000) for 3510 atoms. Found 4 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.2044 (Rfree = 0.000) for 3487 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 3641 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3654 seeds are put forward Round 1: 169 peptides, 34 chains. Longest chain 10 peptides. Score 0.274 Round 2: 198 peptides, 31 chains. Longest chain 14 peptides. Score 0.393 Round 3: 189 peptides, 29 chains. Longest chain 15 peptides. Score 0.393 Round 4: 191 peptides, 32 chains. Longest chain 12 peptides. Score 0.362 Round 5: 190 peptides, 28 chains. Longest chain 16 peptides. Score 0.408 Taking the results from Round 5 Chains 28, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8244 restraints for refining 3589 atoms. 7624 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2107 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 37: After refmac, R = 0.1994 (Rfree = 0.000) for 3554 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 38: After refmac, R = 0.1693 (Rfree = 0.000) for 3545 atoms. Found 5 (19 requested) and removed 15 (9 requested) atoms. Cycle 39: After refmac, R = 0.1620 (Rfree = 0.000) for 3528 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1751 (Rfree = 0.000) for 3515 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 3641 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3662 seeds are put forward Round 1: 167 peptides, 33 chains. Longest chain 9 peptides. Score 0.280 Round 2: 222 peptides, 42 chains. Longest chain 10 peptides. Score 0.328 Round 3: 215 peptides, 36 chains. Longest chain 10 peptides. Score 0.379 Round 4: 204 peptides, 31 chains. Longest chain 16 peptides. Score 0.409 Round 5: 206 peptides, 34 chains. Longest chain 16 peptides. Score 0.379 Taking the results from Round 4 Chains 31, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6233 reflections ( 99.58 % complete ) and 8576 restraints for refining 3669 atoms. 7915 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2225 (Rfree = 0.000) for 3669 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 42: After refmac, R = 0.2176 (Rfree = 0.000) for 3647 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 43: After refmac, R = 0.2127 (Rfree = 0.000) for 3628 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 44: After refmac, R = 0.2068 (Rfree = 0.000) for 3611 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 45: After refmac, R = 0.1751 (Rfree = 0.000) for 3593 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3722 seeds are put forward Round 1: 160 peptides, 37 chains. Longest chain 7 peptides. Score 0.206 Round 2: 167 peptides, 33 chains. Longest chain 10 peptides. Score 0.280 Round 3: 161 peptides, 30 chains. Longest chain 14 peptides. Score 0.301 Round 4: 169 peptides, 31 chains. Longest chain 16 peptides. Score 0.312 Round 5: 165 peptides, 32 chains. Longest chain 13 peptides. Score 0.287 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 138, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (138 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6233 reflections ( 99.58 % complete ) and 8492 restraints for refining 3555 atoms. 7953 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2257 (Rfree = 0.000) for 3555 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2236 (Rfree = 0.000) for 3530 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2169 (Rfree = 0.000) for 3508 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2288 (Rfree = 0.000) for 3488 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:05:28 GMT 2018 Job finished. TimeTaking 38.96 Used memory is bytes: 13041632