Mon 24 Dec 00:48:28 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 2o08-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-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/2o08-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-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 00:48:33 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/2o08-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-3.4-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 376 and 0 Target number of residues in the AU: 376 Target solvent content: 0.6264 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.4-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.90 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: 83.235 3.400 Wilson plot Bfac: 64.48 7673 reflections ( 98.01 % complete ) and 0 restraints for refining 3328 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3156 (Rfree = 0.000) for 3328 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.79 Search for helices and strands: 0 residues in 0 chains, 3422 seeds are put forward NCS extension: 0 residues added, 3422 seeds are put forward Round 1: 217 peptides, 36 chains. Longest chain 14 peptides. Score 0.410 Round 2: 234 peptides, 30 chains. Longest chain 16 peptides. Score 0.529 Round 3: 256 peptides, 31 chains. Longest chain 26 peptides. Score 0.571 Round 4: 250 peptides, 31 chains. Longest chain 22 peptides. Score 0.557 Round 5: 251 peptides, 26 chains. Longest chain 35 peptides. Score 0.613 Taking the results from Round 5 Chains 30, Residues 225, Estimated correctness of the model 32.9 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5496 restraints for refining 2734 atoms. 4515 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3006 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 2: After refmac, R = 0.2960 (Rfree = 0.000) for 2701 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 3: After refmac, R = 0.2789 (Rfree = 0.000) for 2679 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.2859 (Rfree = 0.000) for 2653 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 5: After refmac, R = 0.2776 (Rfree = 0.000) for 2637 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 2.92 Search for helices and strands: 0 residues in 0 chains, 2761 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 2796 seeds are put forward Round 1: 210 peptides, 33 chains. Longest chain 16 peptides. Score 0.427 Round 2: 223 peptides, 30 chains. Longest chain 16 peptides. Score 0.501 Round 3: 229 peptides, 28 chains. Longest chain 24 peptides. Score 0.539 Round 4: 236 peptides, 28 chains. Longest chain 20 peptides. Score 0.557 Round 5: 233 peptides, 25 chains. Longest chain 33 peptides. Score 0.583 Taking the results from Round 5 Chains 25, Residues 208, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6031 restraints for refining 2735 atoms. 5224 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3075 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 7: After refmac, R = 0.3132 (Rfree = 0.000) for 2697 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 8: After refmac, R = 0.2741 (Rfree = 0.000) for 2675 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 9: After refmac, R = 0.2708 (Rfree = 0.000) for 2663 atoms. Found 18 (20 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.2628 (Rfree = 0.000) for 2659 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 2.78 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward NCS extension: 48 residues added (1 deleted due to clashes), 2868 seeds are put forward Round 1: 220 peptides, 36 chains. Longest chain 12 peptides. Score 0.418 Round 2: 239 peptides, 33 chains. Longest chain 25 peptides. Score 0.507 Round 3: 234 peptides, 31 chains. Longest chain 32 peptides. Score 0.517 Round 4: 240 peptides, 28 chains. Longest chain 25 peptides. Score 0.566 Round 5: 230 peptides, 28 chains. Longest chain 36 peptides. Score 0.542 Taking the results from Round 4 Chains 28, Residues 212, Estimated correctness of the model 17.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5885 restraints for refining 2735 atoms. 5065 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2841 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 12: After refmac, R = 0.2653 (Rfree = 0.000) for 2701 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.2345 (Rfree = 0.000) for 2696 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.2293 (Rfree = 0.000) for 2686 atoms. Found 14 (20 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2268 (Rfree = 0.000) for 2684 atoms. Found 3 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 2.78 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 2858 seeds are put forward Round 1: 211 peptides, 33 chains. Longest chain 14 peptides. Score 0.430 Round 2: 237 peptides, 29 chains. Longest chain 26 peptides. Score 0.548 Round 3: 246 peptides, 27 chains. Longest chain 34 peptides. Score 0.591 Round 4: 234 peptides, 28 chains. Longest chain 18 peptides. Score 0.552 Round 5: 229 peptides, 28 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 3 Chains 27, Residues 219, Estimated correctness of the model 25.7 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5415 restraints for refining 2734 atoms. 4409 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2934 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 17: After refmac, R = 0.2743 (Rfree = 0.000) for 2710 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 18: After refmac, R = 0.2711 (Rfree = 0.000) for 2700 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.2550 (Rfree = 0.000) for 2702 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 20: After refmac, R = 0.2461 (Rfree = 0.000) for 2702 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward NCS extension: 48 residues added (7 deleted due to clashes), 2883 seeds are put forward Round 1: 235 peptides, 39 chains. Longest chain 15 peptides. Score 0.424 Round 2: 246 peptides, 34 chains. Longest chain 19 peptides. Score 0.514 Round 3: 239 peptides, 35 chains. Longest chain 15 peptides. Score 0.484 Round 4: 253 peptides, 36 chains. Longest chain 15 peptides. Score 0.509 Round 5: 233 peptides, 28 chains. Longest chain 16 peptides. Score 0.549 Taking the results from Round 5 Chains 28, Residues 205, Estimated correctness of the model 11.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6029 restraints for refining 2735 atoms. 5237 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3088 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 22: After refmac, R = 0.2949 (Rfree = 0.000) for 2716 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 23: After refmac, R = 0.2888 (Rfree = 0.000) for 2697 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.2908 (Rfree = 0.000) for 2694 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 25: After refmac, R = 0.2816 (Rfree = 0.000) for 2686 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.22 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2855 seeds are put forward Round 1: 184 peptides, 31 chains. Longest chain 11 peptides. Score 0.376 Round 2: 197 peptides, 31 chains. Longest chain 13 peptides. Score 0.415 Round 3: 213 peptides, 29 chains. Longest chain 19 peptides. Score 0.486 Round 4: 211 peptides, 30 chains. Longest chain 18 peptides. Score 0.468 Round 5: 219 peptides, 32 chains. Longest chain 17 peptides. Score 0.465 Taking the results from Round 3 Chains 30, Residues 184, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6084 restraints for refining 2735 atoms. 5348 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2848 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 27: After refmac, R = 0.2721 (Rfree = 0.000) for 2719 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 28: After refmac, R = 0.2704 (Rfree = 0.000) for 2710 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 29: After refmac, R = 0.2626 (Rfree = 0.000) for 2701 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 30: After refmac, R = 0.2674 (Rfree = 0.000) for 2699 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2841 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 13 peptides. Score 0.319 Round 2: 216 peptides, 33 chains. Longest chain 14 peptides. Score 0.445 Round 3: 210 peptides, 28 chains. Longest chain 19 peptides. Score 0.490 Round 4: 215 peptides, 31 chains. Longest chain 20 peptides. Score 0.467 Round 5: 208 peptides, 30 chains. Longest chain 20 peptides. Score 0.460 Taking the results from Round 3 Chains 29, Residues 182, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 5822 restraints for refining 2734 atoms. 5037 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2852 (Rfree = 0.000) for 2734 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.2667 (Rfree = 0.000) for 2707 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.2632 (Rfree = 0.000) for 2696 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.2552 (Rfree = 0.000) for 2696 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. Cycle 35: After refmac, R = 0.2530 (Rfree = 0.000) for 2691 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 2.97 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2840 seeds are put forward Round 1: 170 peptides, 32 chains. Longest chain 9 peptides. Score 0.317 Round 2: 195 peptides, 30 chains. Longest chain 20 peptides. Score 0.422 Round 3: 204 peptides, 30 chains. Longest chain 17 peptides. Score 0.448 Round 4: 180 peptides, 25 chains. Longest chain 19 peptides. Score 0.444 Round 5: 187 peptides, 26 chains. Longest chain 19 peptides. Score 0.451 Taking the results from Round 5 Chains 26, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6103 restraints for refining 2735 atoms. 5485 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3088 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 37: After refmac, R = 0.2828 (Rfree = 0.000) for 2711 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.2723 (Rfree = 0.000) for 2704 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.2824 (Rfree = 0.000) for 2698 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 40: After refmac, R = 0.2756 (Rfree = 0.000) for 2690 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.50 2.93 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2852 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 8 peptides. Score 0.264 Round 2: 169 peptides, 31 chains. Longest chain 20 peptides. Score 0.328 Round 3: 177 peptides, 30 chains. Longest chain 13 peptides. Score 0.368 Round 4: 191 peptides, 32 chains. Longest chain 16 peptides. Score 0.384 Round 5: 175 peptides, 27 chains. Longest chain 16 peptides. Score 0.403 Taking the results from Round 5 Chains 29, Residues 148, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7673 reflections ( 98.01 % complete ) and 6044 restraints for refining 2735 atoms. 5423 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2803 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 42: After refmac, R = 0.2693 (Rfree = 0.000) for 2717 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 43: After refmac, R = 0.2690 (Rfree = 0.000) for 2701 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.2728 (Rfree = 0.000) for 2700 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 45: After refmac, R = 0.2672 (Rfree = 0.000) for 2688 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.80 Search for helices and strands: 0 residues in 0 chains, 2808 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2827 seeds are put forward Round 1: 133 peptides, 29 chains. Longest chain 7 peptides. Score 0.233 Round 2: 159 peptides, 27 chains. Longest chain 13 peptides. Score 0.352 Round 3: 158 peptides, 27 chains. Longest chain 14 peptides. Score 0.349 Round 4: 176 peptides, 27 chains. Longest chain 15 peptides. Score 0.406 Round 5: 160 peptides, 28 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 149, 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 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7673 reflections ( 98.01 % complete ) and 6198 restraints for refining 2730 atoms. 5629 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2901 (Rfree = 0.000) for 2730 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2995 (Rfree = 0.000) for 2702 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2952 (Rfree = 0.000) for 2667 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2847 (Rfree = 0.000) for 2645 atoms. TimeTaking 42.13