Mon 24 Dec 00:50:57 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 1vp7-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp7-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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/1vp7-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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 00:51:01 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/1vp7-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp7-3.4-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 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-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.4-parrot-mrncs.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 5329 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3062 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 5329 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.84 2.73 Search for helices and strands: 0 residues in 0 chains, 5413 seeds are put forward NCS extension: 0 residues added, 5413 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 15 peptides. Score 0.363 Round 2: 291 peptides, 37 chains. Longest chain 28 peptides. Score 0.530 Round 3: 295 peptides, 36 chains. Longest chain 20 peptides. Score 0.547 Round 4: 320 peptides, 37 chains. Longest chain 25 peptides. Score 0.585 Round 5: 324 peptides, 33 chains. Longest chain 21 peptides. Score 0.625 Taking the results from Round 5 Chains 36, Residues 291, Estimated correctness of the model 36.6 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8058 restraints for refining 3944 atoms. 6761 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2935 (Rfree = 0.000) for 3944 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 2: After refmac, R = 0.2698 (Rfree = 0.000) for 3808 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 3: After refmac, R = 0.2633 (Rfree = 0.000) for 3765 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 4: After refmac, R = 0.2583 (Rfree = 0.000) for 3731 atoms. Found 20 (28 requested) and removed 17 (14 requested) atoms. Cycle 5: After refmac, R = 0.2481 (Rfree = 0.000) for 3699 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.88 2.77 Search for helices and strands: 0 residues in 0 chains, 3868 seeds are put forward NCS extension: 8 residues added (4 deleted due to clashes), 3876 seeds are put forward Round 1: 282 peptides, 38 chains. Longest chain 21 peptides. Score 0.502 Round 2: 310 peptides, 37 chains. Longest chain 28 peptides. Score 0.567 Round 3: 335 peptides, 37 chains. Longest chain 26 peptides. Score 0.612 Round 4: 321 peptides, 39 chains. Longest chain 21 peptides. Score 0.570 Round 5: 321 peptides, 36 chains. Longest chain 26 peptides. Score 0.596 Taking the results from Round 3 Chains 38, Residues 298, Estimated correctness of the model 32.5 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7360 restraints for refining 3691 atoms. 6094 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2823 (Rfree = 0.000) for 3691 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 7: After refmac, R = 0.2775 (Rfree = 0.000) for 3655 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 8: After refmac, R = 0.2694 (Rfree = 0.000) for 3629 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 9: After refmac, R = 0.2541 (Rfree = 0.000) for 3608 atoms. Found 26 (27 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2530 (Rfree = 0.000) for 3605 atoms. Found 21 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.75 2.64 Search for helices and strands: 0 residues in 0 chains, 3766 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3784 seeds are put forward Round 1: 300 peptides, 43 chains. Longest chain 18 peptides. Score 0.492 Round 2: 307 peptides, 34 chains. Longest chain 25 peptides. Score 0.587 Round 3: 319 peptides, 36 chains. Longest chain 24 peptides. Score 0.592 Round 4: 322 peptides, 35 chains. Longest chain 25 peptides. Score 0.606 Round 5: 332 peptides, 36 chains. Longest chain 26 peptides. Score 0.615 Taking the results from Round 5 Chains 38, Residues 296, Estimated correctness of the model 33.4 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7468 restraints for refining 3780 atoms. 6129 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2915 (Rfree = 0.000) for 3780 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 12: After refmac, R = 0.2832 (Rfree = 0.000) for 3736 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 13: After refmac, R = 0.2826 (Rfree = 0.000) for 3715 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 14: After refmac, R = 0.2802 (Rfree = 0.000) for 3686 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 15: After refmac, R = 0.2727 (Rfree = 0.000) for 3668 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.85 2.74 Search for helices and strands: 0 residues in 0 chains, 3809 seeds are put forward NCS extension: 6 residues added (4 deleted due to clashes), 3815 seeds are put forward Round 1: 313 peptides, 41 chains. Longest chain 17 peptides. Score 0.537 Round 2: 321 peptides, 40 chains. Longest chain 22 peptides. Score 0.562 Round 3: 306 peptides, 36 chains. Longest chain 18 peptides. Score 0.568 Round 4: 294 peptides, 35 chains. Longest chain 25 peptides. Score 0.554 Round 5: 290 peptides, 36 chains. Longest chain 21 peptides. Score 0.537 Taking the results from Round 3 Chains 36, Residues 270, Estimated correctness of the model 17.8 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7818 restraints for refining 3740 atoms. 6707 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3106 (Rfree = 0.000) for 3740 atoms. Found 28 (28 requested) and removed 39 (14 requested) atoms. Cycle 17: After refmac, R = 0.2818 (Rfree = 0.000) for 3703 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 18: After refmac, R = 0.2861 (Rfree = 0.000) for 3686 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 19: After refmac, R = 0.2791 (Rfree = 0.000) for 3681 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 20: After refmac, R = 0.2847 (Rfree = 0.000) for 3670 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 2.78 Search for helices and strands: 0 residues in 0 chains, 3846 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 3857 seeds are put forward Round 1: 285 peptides, 38 chains. Longest chain 27 peptides. Score 0.508 Round 2: 313 peptides, 39 chains. Longest chain 23 peptides. Score 0.555 Round 3: 306 peptides, 40 chains. Longest chain 17 peptides. Score 0.532 Round 4: 301 peptides, 40 chains. Longest chain 15 peptides. Score 0.522 Round 5: 309 peptides, 41 chains. Longest chain 19 peptides. Score 0.529 Taking the results from Round 2 Chains 41, Residues 274, Estimated correctness of the model 13.2 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7518 restraints for refining 3756 atoms. 6339 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2747 (Rfree = 0.000) for 3756 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 22: After refmac, R = 0.2696 (Rfree = 0.000) for 3728 atoms. Found 27 (28 requested) and removed 23 (14 requested) atoms. Cycle 23: After refmac, R = 0.2606 (Rfree = 0.000) for 3722 atoms. Found 22 (28 requested) and removed 18 (14 requested) atoms. Cycle 24: After refmac, R = 0.2625 (Rfree = 0.000) for 3713 atoms. Found 24 (28 requested) and removed 19 (14 requested) atoms. Cycle 25: After refmac, R = 0.2529 (Rfree = 0.000) for 3708 atoms. Found 21 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.73 2.62 Search for helices and strands: 0 residues in 0 chains, 3878 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 3898 seeds are put forward Round 1: 271 peptides, 40 chains. Longest chain 24 peptides. Score 0.459 Round 2: 304 peptides, 37 chains. Longest chain 24 peptides. Score 0.555 Round 3: 319 peptides, 41 chains. Longest chain 25 peptides. Score 0.549 Round 4: 317 peptides, 36 chains. Longest chain 31 peptides. Score 0.588 Round 5: 305 peptides, 41 chains. Longest chain 23 peptides. Score 0.521 Taking the results from Round 4 Chains 37, Residues 281, Estimated correctness of the model 24.6 % 3 chains (66 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7359 restraints for refining 3803 atoms. 6023 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2902 (Rfree = 0.000) for 3803 atoms. Found 28 (28 requested) and removed 29 (14 requested) atoms. Cycle 27: After refmac, R = 0.2817 (Rfree = 0.000) for 3770 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 28: After refmac, R = 0.2625 (Rfree = 0.000) for 3739 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 29: After refmac, R = 0.2726 (Rfree = 0.000) for 3728 atoms. Found 28 (28 requested) and removed 20 (14 requested) atoms. Cycle 30: After refmac, R = 0.2703 (Rfree = 0.000) for 3718 atoms. Found 28 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.77 2.66 Search for helices and strands: 0 residues in 0 chains, 3890 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 3925 seeds are put forward Round 1: 276 peptides, 44 chains. Longest chain 18 peptides. Score 0.430 Round 2: 307 peptides, 41 chains. Longest chain 20 peptides. Score 0.525 Round 3: 301 peptides, 34 chains. Longest chain 29 peptides. Score 0.576 Round 4: 305 peptides, 40 chains. Longest chain 26 peptides. Score 0.530 Round 5: 307 peptides, 40 chains. Longest chain 21 peptides. Score 0.534 Taking the results from Round 3 Chains 36, Residues 267, Estimated correctness of the model 20.6 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7740 restraints for refining 3777 atoms. 6579 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2871 (Rfree = 0.000) for 3777 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 32: After refmac, R = 0.2841 (Rfree = 0.000) for 3759 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 33: After refmac, R = 0.2822 (Rfree = 0.000) for 3748 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 34: After refmac, R = 0.2771 (Rfree = 0.000) for 3731 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 35: After refmac, R = 0.2689 (Rfree = 0.000) for 3729 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.72 2.61 Search for helices and strands: 0 residues in 0 chains, 3898 seeds are put forward NCS extension: 7 residues added (11 deleted due to clashes), 3905 seeds are put forward Round 1: 241 peptides, 39 chains. Longest chain 17 peptides. Score 0.400 Round 2: 297 peptides, 46 chains. Longest chain 18 peptides. Score 0.457 Round 3: 302 peptides, 42 chains. Longest chain 24 peptides. Score 0.506 Round 4: 299 peptides, 44 chains. Longest chain 22 peptides. Score 0.481 Round 5: 305 peptides, 38 chains. Longest chain 20 peptides. Score 0.548 Taking the results from Round 5 Chains 38, Residues 267, Estimated correctness of the model 10.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 8356 restraints for refining 3912 atoms. 7246 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3613 (Rfree = 0.000) for 3912 atoms. Found 29 (29 requested) and removed 47 (14 requested) atoms. Cycle 37: After refmac, R = 0.2973 (Rfree = 0.000) for 3866 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 38: After refmac, R = 0.2847 (Rfree = 0.000) for 3837 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. Cycle 39: After refmac, R = 0.2582 (Rfree = 0.000) for 3828 atoms. Found 19 (29 requested) and removed 18 (14 requested) atoms. Cycle 40: After refmac, R = 0.2527 (Rfree = 0.000) for 3813 atoms. Found 13 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.76 2.65 Search for helices and strands: 0 residues in 0 chains, 3980 seeds are put forward NCS extension: 9 residues added (6 deleted due to clashes), 3989 seeds are put forward Round 1: 272 peptides, 42 chains. Longest chain 18 peptides. Score 0.441 Round 2: 293 peptides, 38 chains. Longest chain 18 peptides. Score 0.525 Round 3: 303 peptides, 37 chains. Longest chain 26 peptides. Score 0.553 Round 4: 307 peptides, 35 chains. Longest chain 32 peptides. Score 0.578 Round 5: 300 peptides, 35 chains. Longest chain 27 peptides. Score 0.565 Taking the results from Round 4 Chains 35, Residues 272, Estimated correctness of the model 21.3 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 10256 reflections ( 99.67 % complete ) and 7715 restraints for refining 3836 atoms. 6464 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2896 (Rfree = 0.000) for 3836 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 42: After refmac, R = 0.2593 (Rfree = 0.000) for 3797 atoms. Found 26 (28 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.2527 (Rfree = 0.000) for 3782 atoms. Found 18 (28 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.2537 (Rfree = 0.000) for 3769 atoms. Found 20 (28 requested) and removed 22 (14 requested) atoms. Cycle 45: After refmac, R = 0.2866 (Rfree = 0.000) for 3760 atoms. Found 28 (28 requested) and removed 41 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.77 2.66 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3924 seeds are put forward Round 1: 242 peptides, 37 chains. Longest chain 18 peptides. Score 0.423 Round 2: 261 peptides, 41 chains. Longest chain 17 peptides. Score 0.426 Round 3: 276 peptides, 35 chains. Longest chain 21 peptides. Score 0.518 Round 4: 263 peptides, 35 chains. Longest chain 21 peptides. Score 0.490 Round 5: 265 peptides, 37 chains. Longest chain 15 peptides. Score 0.475 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 241, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence Sequence coverage is 8 % 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 8200 restraints for refining 3826 atoms. 7201 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2910 (Rfree = 0.000) for 3826 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2917 (Rfree = 0.000) for 3794 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2696 (Rfree = 0.000) for 3767 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2502 (Rfree = 0.000) for 3745 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 57.63