Mon 24 Dec 07:30:54 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 2ffj-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-4.0-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/2ffj-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-4.0-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 07:30:59 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/2ffj-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-4.0-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 407 and 0 Target number of residues in the AU: 407 Target solvent content: 0.6717 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-4.0-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: 19 Cell parameters: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-4.0-parrot-noncs.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: 29.898 4.000 Wilson plot Bfac: 93.41 5972 reflections ( 98.65 % complete ) and 0 restraints for refining 5316 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3500 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3927 (Rfree = 0.000) for 5316 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.88 Search for helices and strands: 0 residues in 0 chains, 5441 seeds are put forward NCS extension: 0 residues added, 5441 seeds are put forward Round 1: 152 peptides, 33 chains. Longest chain 7 peptides. Score 0.231 Round 2: 224 peptides, 43 chains. Longest chain 11 peptides. Score 0.315 Round 3: 260 peptides, 41 chains. Longest chain 15 peptides. Score 0.427 Round 4: 261 peptides, 43 chains. Longest chain 17 peptides. Score 0.409 Round 5: 261 peptides, 39 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 5 Chains 39, Residues 222, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 9751 restraints for refining 4087 atoms. 8848 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3328 (Rfree = 0.000) for 4087 atoms. Found 19 (19 requested) and removed 53 (9 requested) atoms. Cycle 2: After refmac, R = 0.3233 (Rfree = 0.000) for 3967 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 3: After refmac, R = 0.3190 (Rfree = 0.000) for 3862 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. Cycle 4: After refmac, R = 0.3303 (Rfree = 0.000) for 3773 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 5: After refmac, R = 0.2859 (Rfree = 0.000) for 3702 atoms. Found 9 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.87 3.77 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3904 seeds are put forward Round 1: 216 peptides, 41 chains. Longest chain 15 peptides. Score 0.317 Round 2: 253 peptides, 40 chains. Longest chain 18 peptides. Score 0.421 Round 3: 274 peptides, 39 chains. Longest chain 17 peptides. Score 0.479 Round 4: 286 peptides, 38 chains. Longest chain 18 peptides. Score 0.515 Round 5: 286 peptides, 37 chains. Longest chain 17 peptides. Score 0.524 Taking the results from Round 5 Chains 37, Residues 249, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8078 restraints for refining 3624 atoms. 7119 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3054 (Rfree = 0.000) for 3624 atoms. Found 12 (17 requested) and removed 53 (8 requested) atoms. Cycle 7: After refmac, R = 0.2831 (Rfree = 0.000) for 3538 atoms. Found 10 (17 requested) and removed 30 (8 requested) atoms. Cycle 8: After refmac, R = 0.2824 (Rfree = 0.000) for 3482 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 9: After refmac, R = 0.2772 (Rfree = 0.000) for 3445 atoms. Found 11 (16 requested) and removed 17 (8 requested) atoms. Cycle 10: After refmac, R = 0.2720 (Rfree = 0.000) for 3418 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 3703 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3730 seeds are put forward Round 1: 250 peptides, 42 chains. Longest chain 13 peptides. Score 0.393 Round 2: 271 peptides, 42 chains. Longest chain 16 peptides. Score 0.442 Round 3: 280 peptides, 42 chains. Longest chain 15 peptides. Score 0.463 Round 4: 281 peptides, 38 chains. Longest chain 22 peptides. Score 0.504 Round 5: 263 peptides, 40 chains. Longest chain 17 peptides. Score 0.444 Taking the results from Round 4 Chains 38, Residues 243, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8277 restraints for refining 3805 atoms. 7304 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2785 (Rfree = 0.000) for 3805 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 12: After refmac, R = 0.2563 (Rfree = 0.000) for 3738 atoms. Found 15 (17 requested) and removed 36 (8 requested) atoms. Cycle 13: After refmac, R = 0.2207 (Rfree = 0.000) for 3697 atoms. Found 3 (17 requested) and removed 26 (8 requested) atoms. Cycle 14: After refmac, R = 0.2086 (Rfree = 0.000) for 3657 atoms. Found 4 (17 requested) and removed 21 (8 requested) atoms. Cycle 15: After refmac, R = 0.2030 (Rfree = 0.000) for 3633 atoms. Found 3 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 3822 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3846 seeds are put forward Round 1: 231 peptides, 44 chains. Longest chain 10 peptides. Score 0.323 Round 2: 257 peptides, 40 chains. Longest chain 18 peptides. Score 0.430 Round 3: 270 peptides, 43 chains. Longest chain 13 peptides. Score 0.430 Round 4: 271 peptides, 41 chains. Longest chain 14 peptides. Score 0.453 Round 5: 259 peptides, 44 chains. Longest chain 10 peptides. Score 0.393 Taking the results from Round 4 Chains 41, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8773 restraints for refining 3899 atoms. 7894 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2801 (Rfree = 0.000) for 3899 atoms. Found 18 (18 requested) and removed 56 (9 requested) atoms. Cycle 17: After refmac, R = 0.2517 (Rfree = 0.000) for 3825 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. Cycle 18: After refmac, R = 0.2569 (Rfree = 0.000) for 3787 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 19: After refmac, R = 0.2504 (Rfree = 0.000) for 3745 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 20: After refmac, R = 0.2539 (Rfree = 0.000) for 3715 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 3930 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3946 seeds are put forward Round 1: 195 peptides, 38 chains. Longest chain 8 peptides. Score 0.295 Round 2: 242 peptides, 43 chains. Longest chain 14 peptides. Score 0.362 Round 3: 234 peptides, 35 chains. Longest chain 12 peptides. Score 0.429 Round 4: 252 peptides, 37 chains. Longest chain 17 peptides. Score 0.450 Round 5: 261 peptides, 41 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 4 Chains 37, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8627 restraints for refining 3864 atoms. 7804 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2698 (Rfree = 0.000) for 3864 atoms. Found 18 (18 requested) and removed 50 (9 requested) atoms. Cycle 22: After refmac, R = 0.2611 (Rfree = 0.000) for 3800 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 23: After refmac, R = 0.2571 (Rfree = 0.000) for 3757 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 24: After refmac, R = 0.2482 (Rfree = 0.000) for 3734 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 25: After refmac, R = 0.2546 (Rfree = 0.000) for 3710 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 3902 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3921 seeds are put forward Round 1: 212 peptides, 40 chains. Longest chain 12 peptides. Score 0.318 Round 2: 264 peptides, 43 chains. Longest chain 16 peptides. Score 0.416 Round 3: 272 peptides, 43 chains. Longest chain 16 peptides. Score 0.435 Round 4: 268 peptides, 42 chains. Longest chain 13 peptides. Score 0.436 Round 5: 279 peptides, 45 chains. Longest chain 17 peptides. Score 0.431 Taking the results from Round 4 Chains 42, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8441 restraints for refining 3813 atoms. 7579 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2894 (Rfree = 0.000) for 3813 atoms. Found 18 (18 requested) and removed 51 (9 requested) atoms. Cycle 27: After refmac, R = 0.2515 (Rfree = 0.000) for 3749 atoms. Found 15 (17 requested) and removed 31 (8 requested) atoms. Cycle 28: After refmac, R = 0.2474 (Rfree = 0.000) for 3710 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 29: After refmac, R = 0.2625 (Rfree = 0.000) for 3680 atoms. Found 12 (17 requested) and removed 26 (8 requested) atoms. Cycle 30: After refmac, R = 0.2424 (Rfree = 0.000) for 3649 atoms. Found 14 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3889 seeds are put forward Round 1: 204 peptides, 40 chains. Longest chain 11 peptides. Score 0.296 Round 2: 241 peptides, 40 chains. Longest chain 19 peptides. Score 0.392 Round 3: 247 peptides, 40 chains. Longest chain 12 peptides. Score 0.407 Round 4: 260 peptides, 41 chains. Longest chain 18 peptides. Score 0.427 Round 5: 230 peptides, 40 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 4 Chains 41, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8517 restraints for refining 3843 atoms. 7682 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2887 (Rfree = 0.000) for 3843 atoms. Found 18 (18 requested) and removed 41 (9 requested) atoms. Cycle 32: After refmac, R = 0.2602 (Rfree = 0.000) for 3788 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 33: After refmac, R = 0.2637 (Rfree = 0.000) for 3750 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.2801 (Rfree = 0.000) for 3734 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 35: After refmac, R = 0.2818 (Rfree = 0.000) for 3712 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 3928 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3955 seeds are put forward Round 1: 207 peptides, 44 chains. Longest chain 11 peptides. Score 0.258 Round 2: 232 peptides, 39 chains. Longest chain 15 peptides. Score 0.381 Round 3: 225 peptides, 37 chains. Longest chain 14 peptides. Score 0.385 Round 4: 231 peptides, 40 chains. Longest chain 13 peptides. Score 0.367 Round 5: 240 peptides, 39 chains. Longest chain 15 peptides. Score 0.400 Taking the results from Round 5 Chains 39, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8627 restraints for refining 3820 atoms. 7862 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2600 (Rfree = 0.000) for 3820 atoms. Found 16 (18 requested) and removed 23 (9 requested) atoms. Cycle 37: After refmac, R = 0.2678 (Rfree = 0.000) for 3788 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. Cycle 38: After refmac, R = 0.2844 (Rfree = 0.000) for 3754 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 39: After refmac, R = 0.2636 (Rfree = 0.000) for 3725 atoms. Found 15 (17 requested) and removed 21 (8 requested) atoms. Cycle 40: After refmac, R = 0.2667 (Rfree = 0.000) for 3702 atoms. Found 12 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3887 seeds are put forward Round 1: 189 peptides, 39 chains. Longest chain 10 peptides. Score 0.266 Round 2: 197 peptides, 37 chains. Longest chain 12 peptides. Score 0.312 Round 3: 210 peptides, 35 chains. Longest chain 12 peptides. Score 0.369 Round 4: 206 peptides, 34 chains. Longest chain 12 peptides. Score 0.370 Round 5: 228 peptides, 37 chains. Longest chain 15 peptides. Score 0.392 Taking the results from Round 5 Chains 37, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5972 reflections ( 98.65 % complete ) and 8540 restraints for refining 3833 atoms. 7813 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2788 (Rfree = 0.000) for 3833 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 42: After refmac, R = 0.2562 (Rfree = 0.000) for 3788 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 43: After refmac, R = 0.2727 (Rfree = 0.000) for 3756 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 44: After refmac, R = 0.2470 (Rfree = 0.000) for 3731 atoms. Found 13 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.2681 (Rfree = 0.000) for 3722 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3886 seeds are put forward Round 1: 164 peptides, 37 chains. Longest chain 8 peptides. Score 0.217 Round 2: 204 peptides, 42 chains. Longest chain 9 peptides. Score 0.273 Round 3: 195 peptides, 37 chains. Longest chain 9 peptides. Score 0.306 Round 4: 199 peptides, 38 chains. Longest chain 10 peptides. Score 0.306 Round 5: 192 peptides, 36 chains. Longest chain 11 peptides. Score 0.310 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 156, 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 2ffj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5972 reflections ( 98.65 % complete ) and 8739 restraints for refining 3798 atoms. 8151 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2821 (Rfree = 0.000) for 3798 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2784 (Rfree = 0.000) for 3769 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2695 (Rfree = 0.000) for 3746 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2815 (Rfree = 0.000) for 3728 atoms. TimeTaking 42.65