Mon 24 Dec 07:35:56 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 2o08-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-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/2o08-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-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 07:36:01 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.2-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 383 and 0 Target number of residues in the AU: 383 Target solvent content: 0.6195 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: 2o08-3.2-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 60.77 9177 reflections ( 98.16 % complete ) and 0 restraints for refining 3359 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3263 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2528 (Rfree = 0.000) for 3359 atoms. Found 12 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.67 Search for helices and strands: 0 residues in 0 chains, 3460 seeds are put forward NCS extension: 0 residues added, 3460 seeds are put forward Round 1: 206 peptides, 38 chains. Longest chain 11 peptides. Score 0.350 Round 2: 246 peptides, 38 chains. Longest chain 15 peptides. Score 0.467 Round 3: 256 peptides, 34 chains. Longest chain 17 peptides. Score 0.539 Round 4: 271 peptides, 32 chains. Longest chain 21 peptides. Score 0.595 Round 5: 285 peptides, 33 chains. Longest chain 23 peptides. Score 0.616 Taking the results from Round 5 Chains 33, Residues 252, Estimated correctness of the model 45.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5630 restraints for refining 2745 atoms. 4655 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2903 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 2: After refmac, R = 0.2719 (Rfree = 0.000) for 2734 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. Cycle 3: After refmac, R = 0.2702 (Rfree = 0.000) for 2728 atoms. Found 18 (24 requested) and removed 15 (12 requested) atoms. Cycle 4: After refmac, R = 0.2813 (Rfree = 0.000) for 2723 atoms. Found 19 (24 requested) and removed 21 (12 requested) atoms. Cycle 5: After refmac, R = 0.2492 (Rfree = 0.000) for 2711 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.76 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 2908 seeds are put forward Round 1: 263 peptides, 39 chains. Longest chain 21 peptides. Score 0.500 Round 2: 280 peptides, 36 chains. Longest chain 20 peptides. Score 0.575 Round 3: 263 peptides, 31 chains. Longest chain 20 peptides. Score 0.588 Round 4: 258 peptides, 36 chains. Longest chain 15 peptides. Score 0.521 Round 5: 267 peptides, 32 chains. Longest chain 18 peptides. Score 0.586 Taking the results from Round 3 Chains 32, Residues 232, Estimated correctness of the model 37.8 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5637 restraints for refining 2746 atoms. 4663 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3000 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 7: After refmac, R = 0.2740 (Rfree = 0.000) for 2737 atoms. Found 24 (24 requested) and removed 14 (12 requested) atoms. Cycle 8: After refmac, R = 0.2667 (Rfree = 0.000) for 2739 atoms. Found 16 (24 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2602 (Rfree = 0.000) for 2741 atoms. Found 11 (24 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2673 (Rfree = 0.000) for 2736 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 2.70 Search for helices and strands: 0 residues in 0 chains, 2879 seeds are put forward NCS extension: 0 residues added, 2879 seeds are put forward Round 1: 245 peptides, 38 chains. Longest chain 26 peptides. Score 0.464 Round 2: 265 peptides, 30 chains. Longest chain 24 peptides. Score 0.602 Round 3: 259 peptides, 33 chains. Longest chain 24 peptides. Score 0.557 Round 4: 251 peptides, 29 chains. Longest chain 19 peptides. Score 0.581 Round 5: 259 peptides, 29 chains. Longest chain 21 peptides. Score 0.599 Taking the results from Round 2 Chains 33, Residues 235, Estimated correctness of the model 41.6 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5459 restraints for refining 2744 atoms. 4398 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3122 (Rfree = 0.000) for 2744 atoms. Found 24 (24 requested) and removed 17 (12 requested) atoms. Cycle 12: After refmac, R = 0.2959 (Rfree = 0.000) for 2749 atoms. Found 17 (24 requested) and removed 12 (12 requested) atoms. Cycle 13: After refmac, R = 0.2868 (Rfree = 0.000) for 2751 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 14: After refmac, R = 0.2751 (Rfree = 0.000) for 2749 atoms. Found 10 (24 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2693 (Rfree = 0.000) for 2745 atoms. Found 7 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 2866 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 2889 seeds are put forward Round 1: 230 peptides, 38 chains. Longest chain 16 peptides. Score 0.422 Round 2: 253 peptides, 35 chains. Longest chain 16 peptides. Score 0.520 Round 3: 253 peptides, 35 chains. Longest chain 20 peptides. Score 0.520 Round 4: 247 peptides, 34 chains. Longest chain 23 peptides. Score 0.516 Round 5: 235 peptides, 29 chains. Longest chain 16 peptides. Score 0.543 Taking the results from Round 5 Chains 30, Residues 206, Estimated correctness of the model 24.8 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5764 restraints for refining 2744 atoms. 4888 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3254 (Rfree = 0.000) for 2744 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 17: After refmac, R = 0.3019 (Rfree = 0.000) for 2748 atoms. Found 10 (24 requested) and removed 12 (12 requested) atoms. Cycle 18: After refmac, R = 0.2928 (Rfree = 0.000) for 2744 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2830 (Rfree = 0.000) for 2738 atoms. Found 7 (24 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2795 (Rfree = 0.000) for 2729 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 2845 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2861 seeds are put forward Round 1: 220 peptides, 36 chains. Longest chain 15 peptides. Score 0.418 Round 2: 225 peptides, 33 chains. Longest chain 17 peptides. Score 0.470 Round 3: 231 peptides, 31 chains. Longest chain 23 peptides. Score 0.510 Round 4: 240 peptides, 29 chains. Longest chain 20 peptides. Score 0.555 Round 5: 246 peptides, 29 chains. Longest chain 23 peptides. Score 0.569 Taking the results from Round 5 Chains 32, Residues 217, Estimated correctness of the model 32.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5726 restraints for refining 2746 atoms. 4798 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3045 (Rfree = 0.000) for 2746 atoms. Found 21 (24 requested) and removed 14 (12 requested) atoms. Cycle 22: After refmac, R = 0.2875 (Rfree = 0.000) for 2743 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.2785 (Rfree = 0.000) for 2733 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2725 (Rfree = 0.000) for 2725 atoms. Found 2 (24 requested) and removed 16 (12 requested) atoms. Cycle 25: After refmac, R = 0.2700 (Rfree = 0.000) for 2705 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 2.80 Search for helices and strands: 0 residues in 0 chains, 2833 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2852 seeds are put forward Round 1: 217 peptides, 35 chains. Longest chain 14 peptides. Score 0.422 Round 2: 231 peptides, 32 chains. Longest chain 16 peptides. Score 0.498 Round 3: 233 peptides, 33 chains. Longest chain 14 peptides. Score 0.491 Round 4: 245 peptides, 33 chains. Longest chain 16 peptides. Score 0.522 Round 5: 230 peptides, 30 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 4 Chains 35, Residues 212, Estimated correctness of the model 18.3 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5739 restraints for refining 2745 atoms. 4848 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3068 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 15 (12 requested) atoms. Cycle 27: After refmac, R = 0.2812 (Rfree = 0.000) for 2741 atoms. Found 15 (24 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2770 (Rfree = 0.000) for 2730 atoms. Found 16 (24 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.2794 (Rfree = 0.000) for 2721 atoms. Found 20 (24 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2664 (Rfree = 0.000) for 2717 atoms. Found 16 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 2842 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2865 seeds are put forward Round 1: 204 peptides, 37 chains. Longest chain 12 peptides. Score 0.357 Round 2: 241 peptides, 34 chains. Longest chain 21 peptides. Score 0.501 Round 3: 230 peptides, 33 chains. Longest chain 15 peptides. Score 0.483 Round 4: 232 peptides, 37 chains. Longest chain 14 peptides. Score 0.440 Round 5: 225 peptides, 32 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 2 Chains 37, Residues 207, Estimated correctness of the model 11.7 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5776 restraints for refining 2745 atoms. 4919 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3086 (Rfree = 0.000) for 2745 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 32: After refmac, R = 0.2891 (Rfree = 0.000) for 2724 atoms. Found 23 (24 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.2658 (Rfree = 0.000) for 2721 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.2572 (Rfree = 0.000) for 2707 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2604 (Rfree = 0.000) for 2690 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2833 seeds are put forward Round 1: 201 peptides, 38 chains. Longest chain 10 peptides. Score 0.335 Round 2: 240 peptides, 37 chains. Longest chain 27 peptides. Score 0.462 Round 3: 230 peptides, 31 chains. Longest chain 28 peptides. Score 0.507 Round 4: 224 peptides, 32 chains. Longest chain 19 peptides. Score 0.479 Round 5: 227 peptides, 30 chains. Longest chain 19 peptides. Score 0.511 Taking the results from Round 5 Chains 31, Residues 197, Estimated correctness of the model 14.9 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 5707 restraints for refining 2746 atoms. 4833 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2904 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2775 (Rfree = 0.000) for 2742 atoms. Found 16 (24 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.2835 (Rfree = 0.000) for 2730 atoms. Found 18 (24 requested) and removed 16 (12 requested) atoms. Cycle 39: After refmac, R = 0.2669 (Rfree = 0.000) for 2716 atoms. Found 20 (24 requested) and removed 17 (12 requested) atoms. Cycle 40: After refmac, R = 0.2673 (Rfree = 0.000) for 2708 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 2.83 Search for helices and strands: 0 residues in 0 chains, 2827 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2848 seeds are put forward Round 1: 195 peptides, 37 chains. Longest chain 10 peptides. Score 0.329 Round 2: 220 peptides, 34 chains. Longest chain 16 peptides. Score 0.443 Round 3: 220 peptides, 34 chains. Longest chain 14 peptides. Score 0.443 Round 4: 212 peptides, 32 chains. Longest chain 13 peptides. Score 0.446 Round 5: 219 peptides, 30 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 5 Chains 30, Residues 189, Estimated correctness of the model 8.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9177 reflections ( 98.16 % complete ) and 6108 restraints for refining 2746 atoms. 5382 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2789 (Rfree = 0.000) for 2746 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. Cycle 42: After refmac, R = 0.2618 (Rfree = 0.000) for 2746 atoms. Found 16 (24 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.2536 (Rfree = 0.000) for 2741 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.2442 (Rfree = 0.000) for 2737 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2431 (Rfree = 0.000) for 2722 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 2.71 Search for helices and strands: 0 residues in 0 chains, 2832 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2855 seeds are put forward Round 1: 192 peptides, 37 chains. Longest chain 12 peptides. Score 0.319 Round 2: 211 peptides, 33 chains. Longest chain 13 peptides. Score 0.430 Round 3: 227 peptides, 34 chains. Longest chain 15 peptides. Score 0.463 Round 4: 217 peptides, 29 chains. Longest chain 16 peptides. Score 0.497 Round 5: 203 peptides, 26 chains. Longest chain 16 peptides. Score 0.496 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 188, Estimated correctness of the model 10.4 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9177 reflections ( 98.16 % complete ) and 5950 restraints for refining 2745 atoms. 5182 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2766 (Rfree = 0.000) for 2745 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2664 (Rfree = 0.000) for 2728 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2580 (Rfree = 0.000) for 2705 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2576 (Rfree = 0.000) for 2686 atoms. TimeTaking 40.92