Sun 23 Dec 23:57:42 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 2ogi-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-1.9-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/2ogi-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-1.9-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 ============================================================ Sun 23 Dec 23:57:46 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/2ogi-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-1.9-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 407 and 0 Target number of residues in the AU: 407 Target solvent content: 0.5013 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-1.9-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.55 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 1 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: 63.833 1.850 Wilson plot Bfac: 23.66 37458 reflections ( 99.89 % complete ) and 0 restraints for refining 3495 atoms. Observations/parameters ratio is 2.68 ------------------------------------------------------ Starting model: R = 0.3206 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2686 (Rfree = 0.000) for 3495 atoms. Found 133 (149 requested) and removed 74 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.07 2.02 NCS extension: 0 residues added, 3554 seeds are put forward Round 1: 306 peptides, 25 chains. Longest chain 37 peptides. Score 0.787 Round 2: 341 peptides, 16 chains. Longest chain 70 peptides. Score 0.884 Round 3: 351 peptides, 14 chains. Longest chain 51 peptides. Score 0.902 Round 4: 361 peptides, 12 chains. Longest chain 68 peptides. Score 0.917 Round 5: 366 peptides, 10 chains. Longest chain 155 peptides. Score 0.928 Taking the results from Round 5 Chains 11, Residues 356, Estimated correctness of the model 99.6 % 6 chains (317 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 185 B and 188 B 9 chains (360 residues) following loop building 4 chains (321 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3987 restraints for refining 3370 atoms. 1201 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2839 (Rfree = 0.000) for 3370 atoms. Found 120 (144 requested) and removed 74 (72 requested) atoms. Cycle 2: After refmac, R = 0.2558 (Rfree = 0.000) for 3400 atoms. Found 89 (143 requested) and removed 43 (73 requested) atoms. Cycle 3: After refmac, R = 0.2386 (Rfree = 0.000) for 3429 atoms. Found 88 (144 requested) and removed 20 (73 requested) atoms. Cycle 4: After refmac, R = 0.2255 (Rfree = 0.000) for 3484 atoms. Found 71 (146 requested) and removed 20 (74 requested) atoms. Cycle 5: After refmac, R = 0.2182 (Rfree = 0.000) for 3525 atoms. Found 61 (148 requested) and removed 21 (75 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.00 1.95 NCS extension: 19 residues added (203 deleted due to clashes), 3586 seeds are put forward Round 1: 370 peptides, 6 chains. Longest chain 117 peptides. Score 0.945 Round 2: 374 peptides, 3 chains. Longest chain 185 peptides. Score 0.956 Round 3: 371 peptides, 7 chains. Longest chain 87 peptides. Score 0.942 Round 4: 373 peptides, 6 chains. Longest chain 170 peptides. Score 0.946 Round 5: 374 peptides, 6 chains. Longest chain 161 peptides. Score 0.947 Taking the results from Round 2 Chains 3, Residues 371, Estimated correctness of the model 99.8 % 2 chains (366 residues) have been docked in sequence Building loops using Loopy2018 3 chains (371 residues) following loop building 2 chains (366 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3705 restraints for refining 3531 atoms. 674 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2243 (Rfree = 0.000) for 3531 atoms. Found 106 (148 requested) and removed 75 (75 requested) atoms. Cycle 7: After refmac, R = 0.2119 (Rfree = 0.000) for 3557 atoms. Found 79 (146 requested) and removed 37 (76 requested) atoms. Cycle 8: After refmac, R = 0.2055 (Rfree = 0.000) for 3592 atoms. Found 68 (147 requested) and removed 32 (76 requested) atoms. Cycle 9: After refmac, R = 0.2004 (Rfree = 0.000) for 3625 atoms. Found 52 (149 requested) and removed 28 (77 requested) atoms. Cycle 10: After refmac, R = 0.1965 (Rfree = 0.000) for 3642 atoms. Found 52 (147 requested) and removed 32 (78 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.99 1.94 NCS extension: 12 residues added (173 deleted due to clashes), 3676 seeds are put forward Round 1: 372 peptides, 5 chains. Longest chain 183 peptides. Score 0.949 Round 2: 373 peptides, 5 chains. Longest chain 117 peptides. Score 0.949 Round 3: 374 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 4: 372 peptides, 6 chains. Longest chain 145 peptides. Score 0.946 Round 5: 375 peptides, 4 chains. Longest chain 186 peptides. Score 0.954 Taking the results from Round 5 Chains 4, Residues 371, Estimated correctness of the model 99.8 % 3 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 B and 80 B 3 chains (373 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3737 restraints for refining 3560 atoms. 694 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2137 (Rfree = 0.000) for 3560 atoms. Found 118 (140 requested) and removed 72 (76 requested) atoms. Cycle 12: After refmac, R = 0.2018 (Rfree = 0.000) for 3604 atoms. Found 78 (139 requested) and removed 31 (77 requested) atoms. Cycle 13: After refmac, R = 0.1964 (Rfree = 0.000) for 3644 atoms. Found 77 (140 requested) and removed 26 (78 requested) atoms. Cycle 14: After refmac, R = 0.1916 (Rfree = 0.000) for 3694 atoms. Found 62 (142 requested) and removed 32 (79 requested) atoms. Cycle 15: After refmac, R = 0.1898 (Rfree = 0.000) for 3716 atoms. Found 73 (140 requested) and removed 36 (79 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.99 1.94 NCS extension: 3 residues added (0 deleted due to clashes), 3757 seeds are put forward Round 1: 372 peptides, 6 chains. Longest chain 121 peptides. Score 0.946 Round 2: 370 peptides, 6 chains. Longest chain 117 peptides. Score 0.945 Round 3: 375 peptides, 5 chains. Longest chain 183 peptides. Score 0.950 Round 4: 374 peptides, 5 chains. Longest chain 162 peptides. Score 0.950 Round 5: 374 peptides, 5 chains. Longest chain 183 peptides. Score 0.950 Taking the results from Round 5 Chains 5, Residues 369, Estimated correctness of the model 99.8 % 4 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 112 A Built loop between residues 185 A and 188 A 3 chains (373 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3738 restraints for refining 3610 atoms. 695 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2073 (Rfree = 0.000) for 3610 atoms. Found 113 (136 requested) and removed 63 (77 requested) atoms. Cycle 17: After refmac, R = 0.1965 (Rfree = 0.000) for 3657 atoms. Found 77 (134 requested) and removed 25 (78 requested) atoms. Cycle 18: After refmac, R = 0.1906 (Rfree = 0.000) for 3706 atoms. Found 61 (136 requested) and removed 31 (79 requested) atoms. Cycle 19: After refmac, R = 0.1873 (Rfree = 0.000) for 3729 atoms. Found 51 (134 requested) and removed 28 (79 requested) atoms. Cycle 20: After refmac, R = 0.1844 (Rfree = 0.000) for 3747 atoms. Found 66 (131 requested) and removed 24 (80 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.00 1.95 NCS extension: 3 residues added (0 deleted due to clashes), 3795 seeds are put forward Round 1: 373 peptides, 6 chains. Longest chain 133 peptides. Score 0.946 Round 2: 374 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 3: 374 peptides, 5 chains. Longest chain 183 peptides. Score 0.950 Round 4: 373 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 5: 373 peptides, 6 chains. Longest chain 183 peptides. Score 0.946 Taking the results from Round 4 Chains 4, Residues 369, Estimated correctness of the model 99.8 % 3 chains (364 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 76 A 3 chains (371 residues) following loop building 2 chains (366 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3790 restraints for refining 3629 atoms. 759 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2070 (Rfree = 0.000) for 3629 atoms. Found 124 (127 requested) and removed 57 (77 requested) atoms. Cycle 22: After refmac, R = 0.1977 (Rfree = 0.000) for 3692 atoms. Found 83 (130 requested) and removed 29 (79 requested) atoms. Cycle 23: After refmac, R = 0.1898 (Rfree = 0.000) for 3745 atoms. Found 56 (131 requested) and removed 30 (80 requested) atoms. Cycle 24: After refmac, R = 0.1849 (Rfree = 0.000) for 3763 atoms. Found 77 (129 requested) and removed 24 (80 requested) atoms. Cycle 25: After refmac, R = 0.1826 (Rfree = 0.000) for 3811 atoms. Found 68 (130 requested) and removed 51 (81 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 1.94 NCS extension: 0 residues added, 3829 seeds are put forward Round 1: 371 peptides, 4 chains. Longest chain 183 peptides. Score 0.952 Round 2: 371 peptides, 4 chains. Longest chain 183 peptides. Score 0.952 Round 3: 372 peptides, 5 chains. Longest chain 183 peptides. Score 0.949 Round 4: 372 peptides, 5 chains. Longest chain 117 peptides. Score 0.949 Round 5: 372 peptides, 4 chains. Longest chain 184 peptides. Score 0.952 Taking the results from Round 5 Chains 4, Residues 368, Estimated correctness of the model 99.8 % 3 chains (362 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 174 B and 178 B 3 chains (371 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3812 restraints for refining 3665 atoms. 785 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2039 (Rfree = 0.000) for 3665 atoms. Found 114 (122 requested) and removed 61 (78 requested) atoms. Cycle 27: After refmac, R = 0.1942 (Rfree = 0.000) for 3713 atoms. Found 69 (121 requested) and removed 25 (79 requested) atoms. Cycle 28: After refmac, R = 0.1883 (Rfree = 0.000) for 3752 atoms. Found 67 (122 requested) and removed 33 (80 requested) atoms. Cycle 29: After refmac, R = 0.1840 (Rfree = 0.000) for 3782 atoms. Found 58 (122 requested) and removed 43 (80 requested) atoms. Cycle 30: After refmac, R = 0.1841 (Rfree = 0.000) for 3787 atoms. Found 70 (120 requested) and removed 35 (81 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 1.94 NCS extension: 0 residues added, 3822 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 2: 373 peptides, 5 chains. Longest chain 183 peptides. Score 0.949 Round 3: 372 peptides, 6 chains. Longest chain 111 peptides. Score 0.946 Round 4: 370 peptides, 5 chains. Longest chain 183 peptides. Score 0.948 Round 5: 373 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Taking the results from Round 5 Chains 4, Residues 369, Estimated correctness of the model 99.8 % 3 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 76 A 3 chains (371 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3796 restraints for refining 3659 atoms. 769 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2027 (Rfree = 0.000) for 3659 atoms. Found 115 (115 requested) and removed 49 (78 requested) atoms. Cycle 32: After refmac, R = 0.1922 (Rfree = 0.000) for 3720 atoms. Found 83 (118 requested) and removed 31 (79 requested) atoms. Cycle 33: After refmac, R = 0.1868 (Rfree = 0.000) for 3769 atoms. Found 60 (119 requested) and removed 38 (80 requested) atoms. Cycle 34: After refmac, R = 0.1840 (Rfree = 0.000) for 3785 atoms. Found 66 (117 requested) and removed 30 (81 requested) atoms. Cycle 35: After refmac, R = 0.1809 (Rfree = 0.000) for 3818 atoms. Found 61 (117 requested) and removed 38 (81 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.99 1.94 NCS extension: 0 residues added, 3842 seeds are put forward Round 1: 374 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 2: 374 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 3: 373 peptides, 5 chains. Longest chain 183 peptides. Score 0.949 Round 4: 374 peptides, 4 chains. Longest chain 183 peptides. Score 0.953 Round 5: 371 peptides, 6 chains. Longest chain 120 peptides. Score 0.945 Taking the results from Round 4 Chains 4, Residues 370, Estimated correctness of the model 99.8 % 3 chains (364 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 B and 55 B 3 chains (372 residues) following loop building 2 chains (366 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3780 restraints for refining 3680 atoms. 745 conditional restraints added. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2021 (Rfree = 0.000) for 3680 atoms. Found 110 (110 requested) and removed 57 (78 requested) atoms. Cycle 37: After refmac, R = 0.1927 (Rfree = 0.000) for 3725 atoms. Found 75 (108 requested) and removed 17 (79 requested) atoms. Cycle 38: After refmac, R = 0.1859 (Rfree = 0.000) for 3778 atoms. Found 67 (109 requested) and removed 24 (80 requested) atoms. Cycle 39: After refmac, R = 0.1834 (Rfree = 0.000) for 3814 atoms. Found 70 (111 requested) and removed 32 (81 requested) atoms. Cycle 40: After refmac, R = 0.1811 (Rfree = 0.000) for 3846 atoms. Found 63 (112 requested) and removed 27 (82 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.00 1.95 NCS extension: 3 residues added (0 deleted due to clashes), 3886 seeds are put forward Round 1: 372 peptides, 6 chains. Longest chain 121 peptides. Score 0.946 Round 2: 374 peptides, 4 chains. Longest chain 184 peptides. Score 0.953 Round 3: 371 peptides, 7 chains. Longest chain 148 peptides. Score 0.942 Round 4: 371 peptides, 6 chains. Longest chain 126 peptides. Score 0.945 Round 5: 367 peptides, 6 chains. Longest chain 118 peptides. Score 0.943 Taking the results from Round 2 Chains 5, Residues 370, Estimated correctness of the model 99.8 % 3 chains (360 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 B and 77 B 3 chains (371 residues) following loop building 2 chains (365 residues) in sequence following loop building ------------------------------------------------------ 37458 reflections ( 99.89 % complete ) and 3820 restraints for refining 3689 atoms. 793 conditional restraints added. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2023 (Rfree = 0.000) for 3689 atoms. Found 107 (107 requested) and removed 59 (78 requested) atoms. Cycle 42: After refmac, R = 0.1925 (Rfree = 0.000) for 3730 atoms. Found 91 (105 requested) and removed 17 (79 requested) atoms. Cycle 43: After refmac, R = 0.1872 (Rfree = 0.000) for 3799 atoms. Found 61 (107 requested) and removed 26 (81 requested) atoms. Cycle 44: After refmac, R = 0.1835 (Rfree = 0.000) for 3825 atoms. Found 52 (108 requested) and removed 26 (82 requested) atoms. Cycle 45: After refmac, R = 0.1809 (Rfree = 0.000) for 3848 atoms. Found 47 (108 requested) and removed 29 (82 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.00 1.95 NCS extension: 0 residues added, 3867 seeds are put forward Round 1: 371 peptides, 5 chains. Longest chain 183 peptides. Score 0.949 Round 2: 373 peptides, 5 chains. Longest chain 149 peptides. Score 0.949 Round 3: 371 peptides, 6 chains. Longest chain 121 peptides. Score 0.945 Round 4: 371 peptides, 6 chains. Longest chain 122 peptides. Score 0.945 Round 5: 369 peptides, 8 chains. Longest chain 107 peptides. Score 0.937 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 368, Estimated correctness of the model 99.8 % 5 chains (364 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 9 A and 14 A Built loop between residues 46 A and 52 A Built loop between residues 85 B and 88 B 2 chains (375 residues) following loop building 2 chains (375 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 37458 reflections ( 99.89 % complete ) and 3092 restraints for refining 3029 atoms. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2788 (Rfree = 0.000) for 3029 atoms. Found 43 (83 requested) and removed 0 (83 requested) atoms. Cycle 47: After refmac, R = 0.2574 (Rfree = 0.000) for 3029 atoms. Found 22 (84 requested) and removed 0 (65 requested) atoms. Cycle 48: After refmac, R = 0.2432 (Rfree = 0.000) for 3029 atoms. Found 13 (84 requested) and removed 3 (66 requested) atoms. Cycle 49: After refmac, R = 0.2398 (Rfree = 0.000) for 3029 atoms. TimeTaking 47.68