null Mon 24 Dec 08:03:37 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 2f4l-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-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/2f4l-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-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 08:03:42 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/2f4l-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-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 1047 and 0 Target number of residues in the AU: 1047 Target solvent content: 0.5611 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-2.5-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: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.65 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: 86.372 2.500 Wilson plot Bfac: 38.78 45394 reflections ( 99.69 % complete ) and 0 restraints for refining 10530 atoms. Observations/parameters ratio is 1.08 ------------------------------------------------------ Starting model: R = 0.3445 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2514 (Rfree = 0.000) for 10530 atoms. Found 95 (190 requested) and removed 132 (95 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.53 2.53 NCS extension: 0 residues added, 10493 seeds are put forward Round 1: 593 peptides, 122 chains. Longest chain 12 peptides. Score 0.312 Round 2: 617 peptides, 105 chains. Longest chain 14 peptides. Score 0.431 Round 3: 685 peptides, 98 chains. Longest chain 19 peptides. Score 0.540 Round 4: 725 peptides, 100 chains. Longest chain 26 peptides. Score 0.571 Round 5: 747 peptides, 99 chains. Longest chain 22 peptides. Score 0.596 Taking the results from Round 5 Chains 100, Residues 648, Estimated correctness of the model 72.5 % 9 chains (77 residues) have been docked in sequence ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 18212 restraints for refining 8904 atoms. 15466 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2912 (Rfree = 0.000) for 8904 atoms. Found 122 (161 requested) and removed 95 (80 requested) atoms. Cycle 2: After refmac, R = 0.2785 (Rfree = 0.000) for 8893 atoms. Found 77 (161 requested) and removed 88 (80 requested) atoms. Cycle 3: After refmac, R = 0.2753 (Rfree = 0.000) for 8851 atoms. Found 81 (161 requested) and removed 80 (80 requested) atoms. Cycle 4: After refmac, R = 0.2683 (Rfree = 0.000) for 8834 atoms. Found 78 (160 requested) and removed 81 (80 requested) atoms. Cycle 5: After refmac, R = 0.2646 (Rfree = 0.000) for 8813 atoms. Found 70 (160 requested) and removed 80 (80 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.55 2.55 NCS extension: 31 residues added (8 deleted due to clashes), 8878 seeds are put forward Round 1: 712 peptides, 97 chains. Longest chain 20 peptides. Score 0.571 Round 2: 774 peptides, 86 chains. Longest chain 28 peptides. Score 0.669 Round 3: 766 peptides, 89 chains. Longest chain 26 peptides. Score 0.651 Round 4: 806 peptides, 91 chains. Longest chain 35 peptides. Score 0.676 Round 5: 780 peptides, 88 chains. Longest chain 28 peptides. Score 0.666 Taking the results from Round 4 Chains 97, Residues 715, Estimated correctness of the model 81.6 % 14 chains (165 residues) have been docked in sequence ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 17292 restraints for refining 8905 atoms. 13963 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2814 (Rfree = 0.000) for 8905 atoms. Found 112 (161 requested) and removed 95 (80 requested) atoms. Cycle 7: After refmac, R = 0.2637 (Rfree = 0.000) for 8902 atoms. Found 68 (161 requested) and removed 80 (80 requested) atoms. Cycle 8: After refmac, R = 0.2557 (Rfree = 0.000) for 8863 atoms. Found 59 (161 requested) and removed 80 (80 requested) atoms. Cycle 9: After refmac, R = 0.2484 (Rfree = 0.000) for 8832 atoms. Found 55 (160 requested) and removed 80 (80 requested) atoms. Cycle 10: After refmac, R = 0.2443 (Rfree = 0.000) for 8797 atoms. Found 57 (159 requested) and removed 80 (79 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.55 2.55 NCS extension: 50 residues added (25 deleted due to clashes), 8850 seeds are put forward Round 1: 727 peptides, 87 chains. Longest chain 30 peptides. Score 0.626 Round 2: 770 peptides, 87 chains. Longest chain 35 peptides. Score 0.662 Round 3: 786 peptides, 82 chains. Longest chain 35 peptides. Score 0.692 Round 4: 812 peptides, 90 chains. Longest chain 37 peptides. Score 0.684 Round 5: 800 peptides, 78 chains. Longest chain 27 peptides. Score 0.716 Taking the results from Round 5 Chains 85, Residues 722, Estimated correctness of the model 85.6 % 9 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 B and 161 B 83 chains (726 residues) following loop building 8 chains (135 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 17354 restraints for refining 8906 atoms. 14110 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2649 (Rfree = 0.000) for 8906 atoms. Found 124 (161 requested) and removed 88 (80 requested) atoms. Cycle 12: After refmac, R = 0.2502 (Rfree = 0.000) for 8922 atoms. Found 71 (159 requested) and removed 81 (81 requested) atoms. Cycle 13: After refmac, R = 0.2444 (Rfree = 0.000) for 8902 atoms. Found 59 (155 requested) and removed 81 (80 requested) atoms. Cycle 14: After refmac, R = 0.2411 (Rfree = 0.000) for 8864 atoms. Found 72 (151 requested) and removed 80 (80 requested) atoms. Cycle 15: After refmac, R = 0.2343 (Rfree = 0.000) for 8842 atoms. Found 56 (147 requested) and removed 80 (80 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.54 2.54 NCS extension: 106 residues added (34 deleted due to clashes), 8966 seeds are put forward Round 1: 758 peptides, 88 chains. Longest chain 26 peptides. Score 0.649 Round 2: 780 peptides, 75 chains. Longest chain 37 peptides. Score 0.712 Round 3: 812 peptides, 84 chains. Longest chain 25 peptides. Score 0.704 Round 4: 797 peptides, 74 chains. Longest chain 35 peptides. Score 0.727 Round 5: 803 peptides, 80 chains. Longest chain 37 peptides. Score 0.711 Taking the results from Round 4 Chains 86, Residues 723, Estimated correctness of the model 86.6 % 13 chains (220 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 A and 201 A 85 chains (729 residues) following loop building 12 chains (228 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 16227 restraints for refining 8906 atoms. 12569 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2653 (Rfree = 0.000) for 8906 atoms. Found 99 (145 requested) and removed 92 (80 requested) atoms. Cycle 17: After refmac, R = 0.2521 (Rfree = 0.000) for 8902 atoms. Found 74 (142 requested) and removed 85 (80 requested) atoms. Cycle 18: After refmac, R = 0.2464 (Rfree = 0.000) for 8879 atoms. Found 58 (138 requested) and removed 82 (80 requested) atoms. Cycle 19: After refmac, R = 0.2434 (Rfree = 0.000) for 8847 atoms. Found 67 (134 requested) and removed 81 (80 requested) atoms. Cycle 20: After refmac, R = 0.2377 (Rfree = 0.000) for 8823 atoms. Found 51 (131 requested) and removed 80 (80 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.53 2.53 NCS extension: 116 residues added (45 deleted due to clashes), 8943 seeds are put forward Round 1: 742 peptides, 82 chains. Longest chain 34 peptides. Score 0.658 Round 2: 794 peptides, 70 chains. Longest chain 54 peptides. Score 0.737 Round 3: 761 peptides, 74 chains. Longest chain 43 peptides. Score 0.701 Round 4: 779 peptides, 75 chains. Longest chain 36 peptides. Score 0.711 Round 5: 791 peptides, 80 chains. Longest chain 33 peptides. Score 0.703 Taking the results from Round 2 Chains 74, Residues 724, Estimated correctness of the model 87.5 % 11 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 195 B and 199 B 73 chains (727 residues) following loop building 10 chains (219 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 16216 restraints for refining 8906 atoms. 12581 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2494 (Rfree = 0.000) for 8906 atoms. Found 94 (129 requested) and removed 92 (80 requested) atoms. Cycle 22: After refmac, R = 0.2415 (Rfree = 0.000) for 8891 atoms. Found 66 (126 requested) and removed 81 (80 requested) atoms. Cycle 23: After refmac, R = 0.2362 (Rfree = 0.000) for 8855 atoms. Found 53 (122 requested) and removed 82 (80 requested) atoms. Cycle 24: After refmac, R = 0.2349 (Rfree = 0.000) for 8819 atoms. Found 60 (118 requested) and removed 80 (80 requested) atoms. Cycle 25: After refmac, R = 0.2326 (Rfree = 0.000) for 8787 atoms. Found 54 (114 requested) and removed 79 (79 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.55 2.55 NCS extension: 146 residues added (96 deleted due to clashes), 8931 seeds are put forward Round 1: 736 peptides, 80 chains. Longest chain 34 peptides. Score 0.661 Round 2: 772 peptides, 70 chains. Longest chain 46 peptides. Score 0.723 Round 3: 778 peptides, 66 chains. Longest chain 36 peptides. Score 0.740 Round 4: 767 peptides, 67 chains. Longest chain 53 peptides. Score 0.729 Round 5: 779 peptides, 64 chains. Longest chain 54 peptides. Score 0.747 Taking the results from Round 5 Chains 71, Residues 715, Estimated correctness of the model 88.3 % 10 chains (233 residues) have been docked in sequence Building loops using Loopy2018 71 chains (715 residues) following loop building 10 chains (233 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 16075 restraints for refining 8906 atoms. 12378 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2459 (Rfree = 0.000) for 8906 atoms. Found 109 (113 requested) and removed 88 (80 requested) atoms. Cycle 27: After refmac, R = 0.2337 (Rfree = 0.000) for 8906 atoms. Found 62 (109 requested) and removed 80 (80 requested) atoms. Cycle 28: After refmac, R = 0.2312 (Rfree = 0.000) for 8878 atoms. Found 51 (106 requested) and removed 80 (80 requested) atoms. Cycle 29: After refmac, R = 0.2297 (Rfree = 0.000) for 8841 atoms. Found 64 (102 requested) and removed 80 (80 requested) atoms. Cycle 30: After refmac, R = 0.2292 (Rfree = 0.000) for 8817 atoms. Found 47 (99 requested) and removed 69 (80 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.53 2.53 NCS extension: 132 residues added (51 deleted due to clashes), 8947 seeds are put forward Round 1: 737 peptides, 67 chains. Longest chain 43 peptides. Score 0.708 Round 2: 769 peptides, 65 chains. Longest chain 43 peptides. Score 0.737 Round 3: 752 peptides, 60 chains. Longest chain 42 peptides. Score 0.742 Round 4: 749 peptides, 62 chains. Longest chain 45 peptides. Score 0.733 Round 5: 750 peptides, 67 chains. Longest chain 34 peptides. Score 0.717 Taking the results from Round 3 Chains 66, Residues 692, Estimated correctness of the model 87.9 % 12 chains (257 residues) have been docked in sequence Building loops using Loopy2018 66 chains (692 residues) following loop building 12 chains (257 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 16024 restraints for refining 8905 atoms. 12312 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2425 (Rfree = 0.000) for 8905 atoms. Found 97 (97 requested) and removed 90 (80 requested) atoms. Cycle 32: After refmac, R = 0.2348 (Rfree = 0.000) for 8902 atoms. Found 80 (93 requested) and removed 80 (80 requested) atoms. Cycle 33: After refmac, R = 0.2288 (Rfree = 0.000) for 8892 atoms. Found 62 (90 requested) and removed 80 (80 requested) atoms. Cycle 34: After refmac, R = 0.2275 (Rfree = 0.000) for 8866 atoms. Found 56 (86 requested) and removed 80 (80 requested) atoms. Cycle 35: After refmac, R = 0.2237 (Rfree = 0.000) for 8832 atoms. Found 67 (83 requested) and removed 80 (80 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.54 2.54 NCS extension: 155 residues added (71 deleted due to clashes), 8982 seeds are put forward Round 1: 737 peptides, 69 chains. Longest chain 39 peptides. Score 0.701 Round 2: 741 peptides, 62 chains. Longest chain 32 peptides. Score 0.728 Round 3: 789 peptides, 66 chains. Longest chain 37 peptides. Score 0.747 Round 4: 796 peptides, 64 chains. Longest chain 54 peptides. Score 0.757 Round 5: 805 peptides, 61 chains. Longest chain 54 peptides. Score 0.771 Taking the results from Round 5 Chains 70, Residues 744, Estimated correctness of the model 90.3 % 13 chains (271 residues) have been docked in sequence Building loops using Loopy2018 70 chains (744 residues) following loop building 13 chains (271 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 15672 restraints for refining 8905 atoms. 11776 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2346 (Rfree = 0.000) for 8905 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 37: After refmac, R = 0.2244 (Rfree = 0.000) for 8893 atoms. Found 54 (80 requested) and removed 81 (80 requested) atoms. Cycle 38: After refmac, R = 0.2229 (Rfree = 0.000) for 8855 atoms. Found 55 (80 requested) and removed 82 (80 requested) atoms. Cycle 39: After refmac, R = 0.2193 (Rfree = 0.000) for 8823 atoms. Found 59 (80 requested) and removed 70 (80 requested) atoms. Cycle 40: After refmac, R = 0.2167 (Rfree = 0.000) for 8807 atoms. Found 38 (79 requested) and removed 54 (79 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.54 2.54 NCS extension: 193 residues added (84 deleted due to clashes), 9004 seeds are put forward Round 1: 747 peptides, 62 chains. Longest chain 57 peptides. Score 0.732 Round 2: 774 peptides, 63 chains. Longest chain 47 peptides. Score 0.746 Round 3: 808 peptides, 58 chains. Longest chain 49 peptides. Score 0.781 Round 4: 787 peptides, 64 chains. Longest chain 54 peptides. Score 0.751 Round 5: 816 peptides, 66 chains. Longest chain 54 peptides. Score 0.763 Taking the results from Round 3 Chains 68, Residues 750, Estimated correctness of the model 91.0 % 19 chains (392 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 225 C and 228 C 67 chains (750 residues) following loop building 18 chains (394 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 14530 restraints for refining 8906 atoms. 10158 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2398 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 92 (80 requested) atoms. Cycle 42: After refmac, R = 0.2283 (Rfree = 0.000) for 8886 atoms. Found 76 (80 requested) and removed 80 (80 requested) atoms. Cycle 43: After refmac, R = 0.2228 (Rfree = 0.000) for 8872 atoms. Found 62 (80 requested) and removed 80 (80 requested) atoms. Cycle 44: After refmac, R = 0.2200 (Rfree = 0.000) for 8845 atoms. Found 53 (80 requested) and removed 80 (80 requested) atoms. Cycle 45: After refmac, R = 0.2200 (Rfree = 0.000) for 8814 atoms. Found 65 (79 requested) and removed 79 (79 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.53 2.53 NCS extension: 104 residues added (41 deleted due to clashes), 8916 seeds are put forward Round 1: 727 peptides, 64 chains. Longest chain 45 peptides. Score 0.711 Round 2: 777 peptides, 58 chains. Longest chain 40 peptides. Score 0.764 Round 3: 776 peptides, 62 chains. Longest chain 39 peptides. Score 0.751 Round 4: 761 peptides, 63 chains. Longest chain 44 peptides. Score 0.738 Round 5: 791 peptides, 65 chains. Longest chain 43 peptides. Score 0.751 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 719, Estimated correctness of the model 89.7 % 14 chains (292 residues) have been docked in sequence Sequence coverage is 40 % Consider running further cycles of model building using 2f4l-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 193 B and 204 B 62 chains (729 residues) following loop building 13 chains (302 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 45394 reflections ( 99.69 % complete ) and 15603 restraints for refining 8906 atoms. 11580 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2345 (Rfree = 0.000) for 8906 atoms. Found 0 (80 requested) and removed 22 (80 requested) atoms. Cycle 47: After refmac, R = 0.2298 (Rfree = 0.000) for 8877 atoms. Found 0 (80 requested) and removed 17 (80 requested) atoms. Cycle 48: After refmac, R = 0.2286 (Rfree = 0.000) for 8854 atoms. Found 0 (80 requested) and removed 20 (80 requested) atoms. Cycle 49: After refmac, R = 0.2243 (Rfree = 0.000) for 8831 atoms. Found 0 (80 requested) and removed 14 (80 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:41:15 GMT 2018 Job finished. TimeTaking 97.63 Used memory is bytes: 5572136