Mon 24 Dec 07:26:23 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pke-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-parrot-noncs ############### 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 07:26:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-parrot-noncs/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 291 and 0 Target number of residues in the AU: 291 Target solvent content: 0.6496 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-3.6-parrot-noncs.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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 3.600 Wilson plot Bfac: 77.87 4971 reflections ( 96.02 % complete ) and 0 restraints for refining 4419 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3149 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2862 (Rfree = 0.000) for 4419 atoms. Found 28 (28 requested) and removed 55 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 4524 seeds are put forward NCS extension: 0 residues added, 4524 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 8 peptides. Score 0.289 Round 2: 191 peptides, 35 chains. Longest chain 15 peptides. Score 0.371 Round 3: 204 peptides, 34 chains. Longest chain 15 peptides. Score 0.432 Round 4: 203 peptides, 33 chains. Longest chain 15 peptides. Score 0.443 Round 5: 207 peptides, 35 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 4 Chains 34, Residues 170, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8378 restraints for refining 3639 atoms. 7620 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2196 (Rfree = 0.000) for 3639 atoms. Found 18 (23 requested) and removed 29 (11 requested) atoms. Cycle 2: After refmac, R = 0.2044 (Rfree = 0.000) for 3571 atoms. Found 16 (23 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2061 (Rfree = 0.000) for 3552 atoms. Found 20 (22 requested) and removed 15 (11 requested) atoms. Cycle 4: After refmac, R = 0.1901 (Rfree = 0.000) for 3548 atoms. Found 9 (22 requested) and removed 18 (11 requested) atoms. Cycle 5: After refmac, R = 0.1655 (Rfree = 0.000) for 3528 atoms. Found 2 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.93 Search for helices and strands: 0 residues in 0 chains, 3648 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3672 seeds are put forward Round 1: 199 peptides, 42 chains. Longest chain 9 peptides. Score 0.291 Round 2: 207 peptides, 38 chains. Longest chain 13 peptides. Score 0.382 Round 3: 200 peptides, 37 chains. Longest chain 11 peptides. Score 0.373 Round 4: 208 peptides, 37 chains. Longest chain 13 peptides. Score 0.401 Round 5: 211 peptides, 37 chains. Longest chain 17 peptides. Score 0.412 Taking the results from Round 5 Chains 39, Residues 174, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8387 restraints for refining 3531 atoms. 7674 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2081 (Rfree = 0.000) for 3531 atoms. Found 21 (22 requested) and removed 27 (11 requested) atoms. Cycle 7: After refmac, R = 0.1945 (Rfree = 0.000) for 3504 atoms. Found 16 (22 requested) and removed 26 (11 requested) atoms. Cycle 8: After refmac, R = 0.1883 (Rfree = 0.000) for 3477 atoms. Found 17 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.1923 (Rfree = 0.000) for 3459 atoms. Found 21 (22 requested) and removed 21 (11 requested) atoms. Cycle 10: After refmac, R = 0.1510 (Rfree = 0.000) for 3452 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3608 seeds are put forward Round 1: 179 peptides, 37 chains. Longest chain 9 peptides. Score 0.294 Round 2: 202 peptides, 37 chains. Longest chain 11 peptides. Score 0.380 Round 3: 195 peptides, 36 chains. Longest chain 11 peptides. Score 0.370 Round 4: 190 peptides, 35 chains. Longest chain 11 peptides. Score 0.367 Round 5: 203 peptides, 35 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Chains 35, Residues 168, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8223 restraints for refining 3473 atoms. 7540 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1994 (Rfree = 0.000) for 3473 atoms. Found 16 (22 requested) and removed 26 (11 requested) atoms. Cycle 12: After refmac, R = 0.2072 (Rfree = 0.000) for 3448 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 13: After refmac, R = 0.1961 (Rfree = 0.000) for 3441 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 14: After refmac, R = 0.1509 (Rfree = 0.000) for 3430 atoms. Found 7 (22 requested) and removed 15 (11 requested) atoms. Cycle 15: After refmac, R = 0.1408 (Rfree = 0.000) for 3416 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 3590 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3608 seeds are put forward Round 1: 162 peptides, 34 chains. Longest chain 8 peptides. Score 0.276 Round 2: 188 peptides, 34 chains. Longest chain 11 peptides. Score 0.375 Round 3: 174 peptides, 30 chains. Longest chain 13 peptides. Score 0.387 Round 4: 185 peptides, 31 chains. Longest chain 15 peptides. Score 0.411 Round 5: 167 peptides, 30 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 4 Chains 31, Residues 154, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8170 restraints for refining 3439 atoms. 7555 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1762 (Rfree = 0.000) for 3439 atoms. Found 20 (22 requested) and removed 27 (11 requested) atoms. Cycle 17: After refmac, R = 0.1979 (Rfree = 0.000) for 3422 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 18: After refmac, R = 0.1831 (Rfree = 0.000) for 3409 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 19: After refmac, R = 0.1944 (Rfree = 0.000) for 3412 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 20: After refmac, R = 0.1731 (Rfree = 0.000) for 3409 atoms. Found 19 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.88 Search for helices and strands: 0 residues in 0 chains, 3572 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3586 seeds are put forward Round 1: 170 peptides, 35 chains. Longest chain 15 peptides. Score 0.291 Round 2: 187 peptides, 35 chains. Longest chain 10 peptides. Score 0.356 Round 3: 185 peptides, 29 chains. Longest chain 16 peptides. Score 0.441 Round 4: 191 peptides, 34 chains. Longest chain 13 peptides. Score 0.386 Round 5: 200 peptides, 35 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 3 Chains 31, Residues 156, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8165 restraints for refining 3483 atoms. 7509 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1885 (Rfree = 0.000) for 3483 atoms. Found 21 (22 requested) and removed 30 (11 requested) atoms. Cycle 22: After refmac, R = 0.1901 (Rfree = 0.000) for 3463 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 23: After refmac, R = 0.1797 (Rfree = 0.000) for 3452 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 3445 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 25: After refmac, R = 0.1827 (Rfree = 0.000) for 3439 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 4.02 Search for helices and strands: 0 residues in 0 chains, 3601 seeds are put forward NCS extension: 0 residues added, 3601 seeds are put forward Round 1: 139 peptides, 30 chains. Longest chain 8 peptides. Score 0.250 Round 2: 169 peptides, 35 chains. Longest chain 7 peptides. Score 0.287 Round 3: 192 peptides, 35 chains. Longest chain 10 peptides. Score 0.374 Round 4: 168 peptides, 29 chains. Longest chain 10 peptides. Score 0.381 Round 5: 175 peptides, 30 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 5 Chains 30, Residues 145, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8346 restraints for refining 3495 atoms. 7779 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1838 (Rfree = 0.000) for 3495 atoms. Found 21 (22 requested) and removed 25 (11 requested) atoms. Cycle 27: After refmac, R = 0.1750 (Rfree = 0.000) for 3482 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 28: After refmac, R = 0.1767 (Rfree = 0.000) for 3476 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 29: After refmac, R = 0.1701 (Rfree = 0.000) for 3477 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1281 (Rfree = 0.000) for 3482 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 3643 seeds are put forward Round 1: 141 peptides, 31 chains. Longest chain 8 peptides. Score 0.241 Round 2: 153 peptides, 31 chains. Longest chain 8 peptides. Score 0.290 Round 3: 168 peptides, 32 chains. Longest chain 9 peptides. Score 0.332 Round 4: 173 peptides, 32 chains. Longest chain 11 peptides. Score 0.351 Round 5: 167 peptides, 32 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 4 Chains 32, Residues 141, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8378 restraints for refining 3510 atoms. 7835 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1735 (Rfree = 0.000) for 3510 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 32: After refmac, R = 0.1759 (Rfree = 0.000) for 3491 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 33: After refmac, R = 0.1886 (Rfree = 0.000) for 3485 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 34: After refmac, R = 0.1670 (Rfree = 0.000) for 3478 atoms. Found 19 (22 requested) and removed 14 (11 requested) atoms. Cycle 35: After refmac, R = 0.1739 (Rfree = 0.000) for 3476 atoms. Found 22 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 3651 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 3661 seeds are put forward Round 1: 139 peptides, 31 chains. Longest chain 7 peptides. Score 0.232 Round 2: 153 peptides, 30 chains. Longest chain 9 peptides. Score 0.307 Round 3: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.312 Round 4: 145 peptides, 26 chains. Longest chain 11 peptides. Score 0.343 Round 5: 145 peptides, 26 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 5 Chains 26, Residues 119, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8244 restraints for refining 3443 atoms. 7772 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1676 (Rfree = 0.000) for 3443 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.1719 (Rfree = 0.000) for 3435 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.1757 (Rfree = 0.000) for 3437 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 39: After refmac, R = 0.1573 (Rfree = 0.000) for 3438 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 40: After refmac, R = 0.1644 (Rfree = 0.000) for 3442 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 3588 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3591 seeds are put forward Round 1: 111 peptides, 25 chains. Longest chain 7 peptides. Score 0.218 Round 2: 138 peptides, 28 chains. Longest chain 9 peptides. Score 0.281 Round 3: 138 peptides, 25 chains. Longest chain 11 peptides. Score 0.332 Round 4: 126 peptides, 24 chains. Longest chain 8 peptides. Score 0.301 Round 5: 123 peptides, 23 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 3 Chains 25, Residues 113, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8411 restraints for refining 3475 atoms. 7968 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1564 (Rfree = 0.000) for 3475 atoms. Found 20 (22 requested) and removed 19 (11 requested) atoms. Cycle 42: After refmac, R = 0.1667 (Rfree = 0.000) for 3462 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1546 (Rfree = 0.000) for 3464 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 44: After refmac, R = 0.1627 (Rfree = 0.000) for 3466 atoms. Found 21 (22 requested) and removed 15 (11 requested) atoms. Cycle 45: After refmac, R = 0.1105 (Rfree = 0.000) for 3468 atoms. Found 6 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 0 residues added, 3592 seeds are put forward Round 1: 108 peptides, 25 chains. Longest chain 7 peptides. Score 0.205 Round 2: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.258 Round 3: 105 peptides, 18 chains. Longest chain 16 peptides. Score 0.323 Round 4: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.304 Round 5: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 87, 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 2pke-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4971 reflections ( 96.02 % complete ) and 8576 restraints for refining 3428 atoms. 8246 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1450 (Rfree = 0.000) for 3428 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1593 (Rfree = 0.000) for 3406 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1643 (Rfree = 0.000) for 3390 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1704 (Rfree = 0.000) for 3377 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 37.03