Sun 23 Dec 22:23:02 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 1vp7-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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/1vp7-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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 22:23:12 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/1vp7-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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 570 and 0 Target number of residues in the AU: 570 Target solvent content: 0.5492 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.4-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.60 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: 207.138 3.401 Wilson plot Bfac: 35.36 10256 reflections ( 99.67 % complete ) and 0 restraints for refining 5318 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3102 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3282 (Rfree = 0.000) for 5318 atoms. Found 40 (40 requested) and removed 58 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.90 2.79 Search for helices and strands: 0 residues in 0 chains, 5426 seeds are put forward NCS extension: 0 residues added, 5426 seeds are put forward Round 1: 233 peptides, 40 chains. Longest chain 14 peptides. Score 0.369 Round 2: 262 peptides, 37 chains. Longest chain 14 peptides. Score 0.468 Round 3: 286 peptides, 39 chains. Longest chain 21 peptides. Score 0.501 Round 4: 290 peptides, 33 chains. Longest chain 22 peptides. Score 0.564 Round 5: 310 peptides, 36 chains. Longest chain 27 peptides. Score 0.575 Taking the results from Round 5 Chains 38, Residues 274, Estimated correctness of the model 20.2 % 4 chains (72 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8136 restraints for refining 4064 atoms. 6803 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3256 (Rfree = 0.000) for 4064 atoms. Found 30 (30 requested) and removed 51 (15 requested) atoms. Cycle 2: After refmac, R = 0.3095 (Rfree = 0.000) for 3880 atoms. Found 30 (30 requested) and removed 44 (15 requested) atoms. Cycle 3: After refmac, R = 0.2830 (Rfree = 0.000) for 3808 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 4: After refmac, R = 0.2527 (Rfree = 0.000) for 3765 atoms. Found 21 (28 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.2740 (Rfree = 0.000) for 3740 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.67 2.57 Search for helices and strands: 0 residues in 0 chains, 3891 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3908 seeds are put forward Round 1: 300 peptides, 35 chains. Longest chain 25 peptides. Score 0.565 Round 2: 329 peptides, 37 chains. Longest chain 34 peptides. Score 0.602 Round 3: 335 peptides, 35 chains. Longest chain 29 peptides. Score 0.628 Round 4: 331 peptides, 38 chains. Longest chain 26 peptides. Score 0.597 Round 5: 332 peptides, 34 chains. Longest chain 31 peptides. Score 0.631 Taking the results from Round 5 Chains 42, Residues 298, Estimated correctness of the model 38.4 % 5 chains (92 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7215 restraints for refining 3869 atoms. 5706 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3240 (Rfree = 0.000) for 3869 atoms. Found 29 (29 requested) and removed 45 (14 requested) atoms. Cycle 7: After refmac, R = 0.3041 (Rfree = 0.000) for 3787 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 8: After refmac, R = 0.2901 (Rfree = 0.000) for 3742 atoms. Found 28 (28 requested) and removed 35 (14 requested) atoms. Cycle 9: After refmac, R = 0.2858 (Rfree = 0.000) for 3701 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 10: After refmac, R = 0.2770 (Rfree = 0.000) for 3683 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.80 2.69 Search for helices and strands: 0 residues in 0 chains, 3798 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3809 seeds are put forward Round 1: 295 peptides, 39 chains. Longest chain 22 peptides. Score 0.519 Round 2: 333 peptides, 42 chains. Longest chain 23 peptides. Score 0.567 Round 3: 325 peptides, 37 chains. Longest chain 29 peptides. Score 0.594 Round 4: 324 peptides, 41 chains. Longest chain 26 peptides. Score 0.559 Round 5: 332 peptides, 38 chains. Longest chain 21 peptides. Score 0.599 Taking the results from Round 5 Chains 39, Residues 294, Estimated correctness of the model 28.3 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7645 restraints for refining 3828 atoms. 6328 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2879 (Rfree = 0.000) for 3828 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 12: After refmac, R = 0.2910 (Rfree = 0.000) for 3799 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 13: After refmac, R = 0.2769 (Rfree = 0.000) for 3789 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. Cycle 14: After refmac, R = 0.2788 (Rfree = 0.000) for 3778 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 15: After refmac, R = 0.2623 (Rfree = 0.000) for 3766 atoms. Found 20 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.80 2.69 Search for helices and strands: 0 residues in 0 chains, 3893 seeds are put forward NCS extension: 3 residues added (2 deleted due to clashes), 3896 seeds are put forward Round 1: 300 peptides, 45 chains. Longest chain 20 peptides. Score 0.474 Round 2: 320 peptides, 44 chains. Longest chain 25 peptides. Score 0.524 Round 3: 339 peptides, 44 chains. Longest chain 24 peptides. Score 0.561 Round 4: 332 peptides, 43 chains. Longest chain 23 peptides. Score 0.557 Round 5: 332 peptides, 44 chains. Longest chain 24 peptides. Score 0.548 Taking the results from Round 3 Chains 45, Residues 295, Estimated correctness of the model 15.4 % 2 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7768 restraints for refining 3872 atoms. 6468 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3136 (Rfree = 0.000) for 3872 atoms. Found 29 (29 requested) and removed 39 (14 requested) atoms. Cycle 17: After refmac, R = 0.3183 (Rfree = 0.000) for 3830 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. Cycle 18: After refmac, R = 0.2885 (Rfree = 0.000) for 3794 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 19: After refmac, R = 0.2742 (Rfree = 0.000) for 3781 atoms. Found 15 (28 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.2596 (Rfree = 0.000) for 3765 atoms. Found 13 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.83 2.72 Search for helices and strands: 0 residues in 0 chains, 3902 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 3911 seeds are put forward Round 1: 265 peptides, 42 chains. Longest chain 17 peptides. Score 0.425 Round 2: 304 peptides, 42 chains. Longest chain 29 peptides. Score 0.510 Round 3: 311 peptides, 42 chains. Longest chain 28 peptides. Score 0.524 Round 4: 315 peptides, 41 chains. Longest chain 27 peptides. Score 0.541 Round 5: 319 peptides, 38 chains. Longest chain 27 peptides. Score 0.575 Taking the results from Round 5 Chains 41, Residues 281, Estimated correctness of the model 20.2 % 2 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7900 restraints for refining 3854 atoms. 6653 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2944 (Rfree = 0.000) for 3854 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 22: After refmac, R = 0.2812 (Rfree = 0.000) for 3817 atoms. Found 24 (29 requested) and removed 34 (14 requested) atoms. Cycle 23: After refmac, R = 0.2664 (Rfree = 0.000) for 3783 atoms. Found 26 (28 requested) and removed 22 (14 requested) atoms. Cycle 24: After refmac, R = 0.2776 (Rfree = 0.000) for 3769 atoms. Found 27 (28 requested) and removed 19 (14 requested) atoms. Cycle 25: After refmac, R = 0.2681 (Rfree = 0.000) for 3761 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 2.78 Search for helices and strands: 0 residues in 0 chains, 3908 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3921 seeds are put forward Round 1: 273 peptides, 42 chains. Longest chain 18 peptides. Score 0.443 Round 2: 313 peptides, 45 chains. Longest chain 23 peptides. Score 0.501 Round 3: 296 peptides, 43 chains. Longest chain 18 peptides. Score 0.484 Round 4: 317 peptides, 46 chains. Longest chain 28 peptides. Score 0.500 Round 5: 311 peptides, 43 chains. Longest chain 23 peptides. Score 0.515 Taking the results from Round 5 Chains 43, Residues 268, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8363 restraints for refining 3859 atoms. 7334 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3371 (Rfree = 0.000) for 3859 atoms. Found 29 (29 requested) and removed 49 (14 requested) atoms. Cycle 27: After refmac, R = 0.2910 (Rfree = 0.000) for 3818 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 28: After refmac, R = 0.2737 (Rfree = 0.000) for 3804 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 29: After refmac, R = 0.2565 (Rfree = 0.000) for 3795 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 30: After refmac, R = 0.2474 (Rfree = 0.000) for 3789 atoms. Found 26 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.87 2.76 Search for helices and strands: 0 residues in 0 chains, 3954 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3970 seeds are put forward Round 1: 276 peptides, 46 chains. Longest chain 16 peptides. Score 0.410 Round 2: 304 peptides, 43 chains. Longest chain 19 peptides. Score 0.501 Round 3: 316 peptides, 42 chains. Longest chain 24 peptides. Score 0.534 Round 4: 320 peptides, 40 chains. Longest chain 37 peptides. Score 0.560 Round 5: 327 peptides, 37 chains. Longest chain 24 peptides. Score 0.598 Taking the results from Round 5 Chains 39, Residues 290, Estimated correctness of the model 28.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8128 restraints for refining 3887 atoms. 6945 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2892 (Rfree = 0.000) for 3887 atoms. Found 29 (29 requested) and removed 40 (14 requested) atoms. Cycle 32: After refmac, R = 0.2695 (Rfree = 0.000) for 3853 atoms. Found 27 (29 requested) and removed 20 (14 requested) atoms. Cycle 33: After refmac, R = 0.2579 (Rfree = 0.000) for 3850 atoms. Found 20 (29 requested) and removed 19 (14 requested) atoms. Cycle 34: After refmac, R = 0.2577 (Rfree = 0.000) for 3841 atoms. Found 21 (29 requested) and removed 17 (14 requested) atoms. Cycle 35: After refmac, R = 0.2478 (Rfree = 0.000) for 3838 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.88 2.77 Search for helices and strands: 0 residues in 0 chains, 3942 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 3982 seeds are put forward Round 1: 270 peptides, 42 chains. Longest chain 20 peptides. Score 0.436 Round 2: 295 peptides, 38 chains. Longest chain 17 peptides. Score 0.529 Round 3: 294 peptides, 38 chains. Longest chain 18 peptides. Score 0.527 Round 4: 297 peptides, 38 chains. Longest chain 19 peptides. Score 0.533 Round 5: 276 peptides, 35 chains. Longest chain 20 peptides. Score 0.518 Taking the results from Round 4 Chains 38, Residues 259, Estimated correctness of the model 5.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8375 restraints for refining 3893 atoms. 7377 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2849 (Rfree = 0.000) for 3893 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 37: After refmac, R = 0.2692 (Rfree = 0.000) for 3883 atoms. Found 28 (29 requested) and removed 22 (14 requested) atoms. Cycle 38: After refmac, R = 0.2581 (Rfree = 0.000) for 3878 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 39: After refmac, R = 0.2555 (Rfree = 0.000) for 3867 atoms. Found 27 (29 requested) and removed 21 (14 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2598 (Rfree = 0.000) for 3863 atoms. Found 26 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.84 2.73 Search for helices and strands: 0 residues in 0 chains, 4061 seeds are put forward NCS extension: 9 residues added (2 deleted due to clashes), 4070 seeds are put forward Round 1: 239 peptides, 41 chains. Longest chain 16 peptides. Score 0.373 Round 2: 299 peptides, 42 chains. Longest chain 19 peptides. Score 0.500 Round 3: 298 peptides, 42 chains. Longest chain 20 peptides. Score 0.498 Round 4: 301 peptides, 42 chains. Longest chain 18 peptides. Score 0.504 Round 5: 305 peptides, 41 chains. Longest chain 23 peptides. Score 0.521 Taking the results from Round 5 Chains 41, Residues 264, Estimated correctness of the model 0.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8665 restraints for refining 3968 atoms. 7650 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2762 (Rfree = 0.000) for 3968 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 42: After refmac, R = 0.2549 (Rfree = 0.000) for 3948 atoms. Found 22 (29 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.2523 (Rfree = 0.000) for 3931 atoms. Found 28 (29 requested) and removed 23 (14 requested) atoms. Cycle 44: After refmac, R = 0.2424 (Rfree = 0.000) for 3930 atoms. Found 19 (29 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.2353 (Rfree = 0.000) for 3924 atoms. Found 14 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.84 2.73 Search for helices and strands: 0 residues in 0 chains, 4079 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 4106 seeds are put forward Round 1: 247 peptides, 41 chains. Longest chain 18 peptides. Score 0.393 Round 2: 293 peptides, 38 chains. Longest chain 21 peptides. Score 0.525 Round 3: 281 peptides, 42 chains. Longest chain 16 peptides. Score 0.461 Round 4: 279 peptides, 37 chains. Longest chain 21 peptides. Score 0.505 Round 5: 286 peptides, 36 chains. Longest chain 23 peptides. Score 0.529 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 250, Estimated correctness of the model 3.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vp7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10256 reflections ( 99.67 % complete ) and 8535 restraints for refining 3928 atoms. 7571 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2667 (Rfree = 0.000) for 3928 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2594 (Rfree = 0.000) for 3901 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2512 (Rfree = 0.000) for 3880 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2515 (Rfree = 0.000) for 3864 atoms. TimeTaking 83.03