null Mon 24 Dec 00:13:18 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 2avn-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2avn-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-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/2avn-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-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 00:13:22 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/2avn-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2avn-4.0-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 616 and 0 Target number of residues in the AU: 616 Target solvent content: 0.6578 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 520 Adjusted target solvent content: 0.71 Input MTZ file: 2avn-4.0-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.20 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: 115.845 4.000 Wilson plot Bfac: 83.40 8899 reflections ( 99.49 % complete ) and 0 restraints for refining 4585 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3654 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3515 (Rfree = 0.000) for 4585 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 2.80 Search for helices and strands: 0 residues in 0 chains, 4725 seeds are put forward NCS extension: 0 residues added, 4725 seeds are put forward Round 1: 280 peptides, 41 chains. Longest chain 19 peptides. Score 0.403 Round 2: 310 peptides, 30 chains. Longest chain 31 peptides. Score 0.533 Round 3: 314 peptides, 28 chains. Longest chain 28 peptides. Score 0.553 Round 4: 318 peptides, 35 chains. Longest chain 17 peptides. Score 0.509 Round 5: 320 peptides, 33 chains. Longest chain 20 peptides. Score 0.526 Taking the results from Round 3 Chains 31, Residues 286, Estimated correctness of the model 0.0 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8852 restraints for refining 4041 atoms. 7576 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2816 (Rfree = 0.000) for 4041 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 2: After refmac, R = 0.2672 (Rfree = 0.000) for 3989 atoms. Found 14 (19 requested) and removed 13 (9 requested) atoms. Cycle 3: After refmac, R = 0.2461 (Rfree = 0.000) for 3968 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. Cycle 4: After refmac, R = 0.2450 (Rfree = 0.000) for 3945 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2489 (Rfree = 0.000) for 3923 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 4102 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4125 seeds are put forward Round 1: 328 peptides, 39 chains. Longest chain 25 peptides. Score 0.496 Round 2: 333 peptides, 35 chains. Longest chain 24 peptides. Score 0.531 Round 3: 350 peptides, 33 chains. Longest chain 34 peptides. Score 0.569 Round 4: 343 peptides, 35 chains. Longest chain 33 peptides. Score 0.546 Round 5: 346 peptides, 31 chains. Longest chain 26 peptides. Score 0.576 Taking the results from Round 5 Chains 32, Residues 315, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8195 restraints for refining 3859 atoms. 6830 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3339 (Rfree = 0.000) for 3859 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 7: After refmac, R = 0.2986 (Rfree = 0.000) for 3827 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 8: After refmac, R = 0.2740 (Rfree = 0.000) for 3806 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.2561 (Rfree = 0.000) for 3784 atoms. Found 15 (18 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2446 (Rfree = 0.000) for 3776 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 2.84 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 0 residues added, 3925 seeds are put forward Round 1: 315 peptides, 36 chains. Longest chain 21 peptides. Score 0.497 Round 2: 338 peptides, 38 chains. Longest chain 18 peptides. Score 0.518 Round 3: 332 peptides, 32 chains. Longest chain 26 peptides. Score 0.551 Round 4: 334 peptides, 35 chains. Longest chain 34 peptides. Score 0.533 Round 5: 332 peptides, 29 chains. Longest chain 25 peptides. Score 0.571 Taking the results from Round 5 Chains 30, Residues 303, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8585 restraints for refining 3883 atoms. 7348 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3345 (Rfree = 0.000) for 3883 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 12: After refmac, R = 0.2887 (Rfree = 0.000) for 3842 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.2826 (Rfree = 0.000) for 3831 atoms. Found 10 (18 requested) and removed 15 (9 requested) atoms. Cycle 14: After refmac, R = 0.2814 (Rfree = 0.000) for 3814 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.2920 (Rfree = 0.000) for 3801 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.89 2.89 Search for helices and strands: 0 residues in 0 chains, 3973 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3992 seeds are put forward Round 1: 324 peptides, 42 chains. Longest chain 30 peptides. Score 0.468 Round 2: 317 peptides, 31 chains. Longest chain 27 peptides. Score 0.536 Round 3: 326 peptides, 33 chains. Longest chain 26 peptides. Score 0.535 Round 4: 328 peptides, 30 chains. Longest chain 33 peptides. Score 0.559 Round 5: 326 peptides, 29 chains. Longest chain 34 peptides. Score 0.563 Taking the results from Round 5 Chains 29, Residues 297, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8304 restraints for refining 3757 atoms. 7145 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2978 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2739 (Rfree = 0.000) for 3726 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2752 (Rfree = 0.000) for 3724 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.2716 (Rfree = 0.000) for 3714 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.2670 (Rfree = 0.000) for 3706 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 2.84 Search for helices and strands: 0 residues in 0 chains, 3833 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3852 seeds are put forward Round 1: 307 peptides, 41 chains. Longest chain 17 peptides. Score 0.448 Round 2: 330 peptides, 33 chains. Longest chain 28 peptides. Score 0.541 Round 3: 303 peptides, 35 chains. Longest chain 20 peptides. Score 0.486 Round 4: 320 peptides, 31 chains. Longest chain 43 peptides. Score 0.540 Round 5: 323 peptides, 34 chains. Longest chain 25 peptides. Score 0.524 Taking the results from Round 2 Chains 36, Residues 297, Estimated correctness of the model 0.0 % 2 chains (43 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7775 restraints for refining 3757 atoms. 6423 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2955 (Rfree = 0.000) for 3757 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.2789 (Rfree = 0.000) for 3731 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2759 (Rfree = 0.000) for 3726 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2713 (Rfree = 0.000) for 3715 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2686 (Rfree = 0.000) for 3704 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 2.82 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3894 seeds are put forward Round 1: 295 peptides, 38 chains. Longest chain 21 peptides. Score 0.451 Round 2: 310 peptides, 30 chains. Longest chain 33 peptides. Score 0.533 Round 3: 312 peptides, 31 chains. Longest chain 26 peptides. Score 0.529 Round 4: 306 peptides, 32 chains. Longest chain 25 peptides. Score 0.513 Round 5: 310 peptides, 29 chains. Longest chain 26 peptides. Score 0.540 Taking the results from Round 5 Chains 29, Residues 281, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8304 restraints for refining 3786 atoms. 7103 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3366 (Rfree = 0.000) for 3786 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 27: After refmac, R = 0.2918 (Rfree = 0.000) for 3753 atoms. Found 15 (18 requested) and removed 14 (9 requested) atoms. Cycle 28: After refmac, R = 0.2749 (Rfree = 0.000) for 3737 atoms. Found 11 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2610 (Rfree = 0.000) for 3728 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2463 (Rfree = 0.000) for 3723 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 3901 seeds are put forward Round 1: 302 peptides, 41 chains. Longest chain 25 peptides. Score 0.440 Round 2: 322 peptides, 34 chains. Longest chain 28 peptides. Score 0.522 Round 3: 337 peptides, 29 chains. Longest chain 28 peptides. Score 0.578 Round 4: 307 peptides, 29 chains. Longest chain 24 peptides. Score 0.536 Round 5: 316 peptides, 33 chains. Longest chain 22 peptides. Score 0.521 Taking the results from Round 3 Chains 30, Residues 308, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8156 restraints for refining 3756 atoms. 6905 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3301 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.2830 (Rfree = 0.000) for 3731 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 33: After refmac, R = 0.2831 (Rfree = 0.000) for 3713 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.2778 (Rfree = 0.000) for 3687 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2646 (Rfree = 0.000) for 3675 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 2.83 Search for helices and strands: 0 residues in 0 chains, 3819 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3838 seeds are put forward Round 1: 297 peptides, 46 chains. Longest chain 15 peptides. Score 0.393 Round 2: 316 peptides, 38 chains. Longest chain 20 peptides. Score 0.484 Round 3: 319 peptides, 36 chains. Longest chain 22 peptides. Score 0.504 Round 4: 331 peptides, 31 chains. Longest chain 26 peptides. Score 0.556 Round 5: 331 peptides, 36 chains. Longest chain 23 peptides. Score 0.521 Taking the results from Round 4 Chains 32, Residues 300, Estimated correctness of the model 0.0 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 7780 restraints for refining 3756 atoms. 6388 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3137 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2844 (Rfree = 0.000) for 3730 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 38: After refmac, R = 0.2855 (Rfree = 0.000) for 3715 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2727 (Rfree = 0.000) for 3705 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.2729 (Rfree = 0.000) for 3692 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 2.77 Search for helices and strands: 0 residues in 0 chains, 3839 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3867 seeds are put forward Round 1: 290 peptides, 42 chains. Longest chain 17 peptides. Score 0.412 Round 2: 305 peptides, 34 chains. Longest chain 28 peptides. Score 0.497 Round 3: 308 peptides, 35 chains. Longest chain 23 peptides. Score 0.494 Round 4: 304 peptides, 32 chains. Longest chain 26 peptides. Score 0.510 Round 5: 308 peptides, 36 chains. Longest chain 20 peptides. Score 0.487 Taking the results from Round 4 Chains 34, Residues 272, Estimated correctness of the model 0.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8899 reflections ( 99.49 % complete ) and 8137 restraints for refining 3756 atoms. 6928 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3249 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2954 (Rfree = 0.000) for 3726 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 43: After refmac, R = 0.2867 (Rfree = 0.000) for 3702 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 44: After refmac, R = 0.2638 (Rfree = 0.000) for 3688 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2577 (Rfree = 0.000) for 3679 atoms. Found 8 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 2.78 Search for helices and strands: 0 residues in 0 chains, 3824 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 3854 seeds are put forward Round 1: 239 peptides, 40 chains. Longest chain 15 peptides. Score 0.337 Round 2: 259 peptides, 34 chains. Longest chain 22 peptides. Score 0.423 Round 3: 268 peptides, 34 chains. Longest chain 25 peptides. Score 0.438 Round 4: 272 peptides, 32 chains. Longest chain 20 peptides. Score 0.460 Round 5: 278 peptides, 35 chains. Longest chain 20 peptides. Score 0.446 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 240, 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 2avn-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8899 reflections ( 99.49 % complete ) and 8900 restraints for refining 3757 atoms. 7972 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3367 (Rfree = 0.000) for 3757 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2861 (Rfree = 0.000) for 3721 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2845 (Rfree = 0.000) for 3692 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2470 (Rfree = 0.000) for 3660 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:01:40 GMT 2018 Job finished. TimeTaking 48.37 Used memory is bytes: 18359984